Supplementary Information a Novel Algorithm for Simplification Of

Supplementary Information

A novel algorithm for simplification of complex gene classifiers

Raphael A. Wilson1, Ling Teng2, Karen M. Bachmeyer2, Mei Lin Z. Bissonnette3, Aliya N. Husain3, David M.

Parham4, Timothy J. Triche5, Michele R. Wing6, Julie M. Gastier-Foster6, Frederic G. Barr7, Douglas S.

Hawkins8, James R. Anderson9, Stephen X. Skapek1,*, and Samuel L. Volchenboum2,10,11,*

1Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical

Center and Children’s Medical Center, Dallas, TX; 4Department of Pathology, University of Oklahoma Health

Sciences Center, Oklahoma City, OK; 5Department of Pathology, University of Southern California and

Children’s Hospital of Los Angeles, Los Angeles, CA; 6Department of Pathology and Laboratory Medicine,

Nationwide Children's Hospital, Columbus, OH and Department of Pathology and Pediatrics, The Ohio

State University, Columbus, OH; 7National Cancer Institute, Bethesda, MD; 8Division of Hematology/

Oncology, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA;

9Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE; and 2The Section of Pediatric Hematology/Oncology, Department of Pediatrics, 3Department of Pathology,

10Center for Research Informatics, and 11The Computation Institute, University of Chicago, Chicago, IL

*For correspondence: [email protected] or [email protected].

1 Table of Contents

Supplementary Figure 1 Two-gene combinations from the 50-gene F1/F2 classifier with >98% 3 classification efficiency in the Williamson data set Supplementary Figure 2 Thirteen two-gene combinations with >99% classification efficiency, 4 identified from exhaustive analysis of top 2000 genes Supplementary Figure 3 Gene dyads with classification efficiency >95% identified through 5 exhaustive search of all possible combinations Supplementary Figure 4 Detection of gene expression is comparable for fresh-frozen and 6 paraformaldehyde-fixed material with nCounter Supplementary Figure 5 Gene expression detected in each case with the Williamson F1/F2 7 metagene nCounter Code set Supplementary Table 1 Four-gene combinations with ≥ 99% accuracy 8

Supplementary Table 2 Dyad classifiers from T-test ranking of Williamson data set with ≥ 98% 21 accuracy, applied to Davicioni data Supplementary Table 3 T-test dyad classifier genes found in F1/F2 metagenes (L) and F1/F2 70 metagene probes excluded from dyad pairs (R) Supplementary Table 4 Top-scoring classifiers from exhaustive search of 1.5 billion gene pairs from 71 Williamson data set, also applied to Davicioni and Exon data Supplementary Table 5 Tumor sample characteristics 72

Supplementary Table 6 Genes in nCounter set 73

Supplementary Table 7 PCA Scores by tumor sample for nCounter Data 74

Supplementary Table 8 CA Loadings for nCounter Data 75

Supplementary Table 9 Top-scoring nCounter dyad classifiers 76

Supplementary Table 10 Top gene combinations - Lung cancer data 77

2 Supplementary Figure 1. Two-gene combinations from the 50-gene F1/F2 classifier with >98% classification efficiency in the Williamson data set.

An exhaustive search of two-gene combinations from the fifty Williamson F1/F2 classifier genes was performed using support vector classification (SVC). Ten dyads with a classification efficiency of >98% are shown. Fusion positive samples are indicated in pink and fusion negative samples in blue. The PAX3-NCOA1 sample (green) clusters with the fusion negative samples using these gene dyads. 3 Supplementary Figure 2. Thirteen two-gene combinations with >99% classification efficiency, identified from exhaustive analysis of top 2000 genes

1.5 1.5 1.5

1.0 1.0 1.0

PIPOX 0.5 PIPOX 0.5 NOS1 0.5 _at _s_at 0 0 _s_at 0

239132 −0.5 221605 −0.5 −0.5 221605

−1.0 −1.0 −1.0

−101234 −10123 −1.5 −1.0 −0.5 0 0.5 1.0 1.5 2.0 225292_at COL27A1 1554500_a_at RGS7 228904_at HOXB3 3.0 2.0 1.5 2.5 2.0 1.5 1.0 1.5 1.0 1.0

PIPOX 0.5 0.5 CELA2A/2B

0.5 ARHGAP26 _s_at 0

0 _at _s_at 0 −0.5

221605 −0.5 −1.0

−0.5 226576 206446 −1.5 −1.0 −1.0 −2.0 −2.5 −2−10123 −2 −1 0 1 2 −1.5 −1.0 −0.5 0 0.5 1.0 1.5 2.0 1568957x_at SRGAP2P1 205150_s_at TRIL 232149_s_at NSMAF 2.5 1.5 2.0 1.5 1.0 1.5 1.0 0.5 1.0

NOS1 0.5 PITPNM3 CELA2A/2B 0.5 _at 0 0 _at _s_at 0 −0.5 239132

−0.5 230076 −0.5 −1.0 206446

−1.0 −1.0 −1.5

−2 −1 0 1 2 −2−10123 −2 −1 0 1 2 3 203737_s_at PPRC1 227083_at B3GALTL 226421_at AMMECR1

1.5 2.0 1.5 1.5 1.0 1.0 1.0

PIPOX 0.5 0.5 SYN2 0.5 NOS1 _at _at _s_at 0 0 0 −0.5 210247 239132

221605 −0.5 −0.5 −1.0 −1.0 −1.5 −1.0

−1012345 −10123 −2−101234 205731_s_at NCOA2 239466_at LOC344595 225263_at HS6ST1

Fusion Positive (PAX3/PAX7) Fusion Positive (NCOA1) Fusion Negative

The genes were sorted by differential expression between fusion positive and fusion negative status using a t-test. The top and bottom 1000 genes from the sorted list were used for an exhaustive analysis of the 1,000,000 possible dyads. Thirteen gene pairs yielded a classification efficiency of greater than 99%. Fusion positive samples are indicated in pink, fusion negative in blue. RGS7 achieved a classification of greater than 99% with two different NOS1 probes, so only one of the plots for this gene dyad is shown. Again, the PAX3-NCOA1 sample (green) clusters with the fusion negative samples using these gene dyads. 4 Supplementary Figure 3. Gene dyads with classification efficiency >95% identified through exhaustive search of all possible combinations

a. 3 95.0% 1 3 99.0% 2 0 2 1 −1 1 0 0 PEG3 EPAS1 −1 −2 THSD4 −1 −2 −3 −3 95.0% −2 −4 −2 −1 0 1 2 −3 −2 −1 0 1 2 −1012 MYCN GPX7 KCND3

b. 3 4 89.5% 1 93.7% 2 3 0 1 2 −1 1 0 PEG3 EPAS1 −2 THSD4 0 −1 −1 −2 −3 89.5% −2 −2−10123 −3 −2 −1 0 1 2 3 −1012 MYCN GPX7 KCND3

c. 3 2 93.8% 1 2 1 1 0 0 0 −1 PEG3 EPAS1 −1 THSD4 −1 −2 −2 −2 −3 −3 93.8% 98.7% −2 −1 0 1 −2 −1 0 1 −1 0 1 2 MYCN GPX7 KCND3

Using a high-performance computing cluster, the 1.5 billion two-gene combinations of all 54,613 genes were searched, and additional discriminating gene pairs were found (Supplementary Table 4). Three examples of dyads with > 95% efficiency are shown in (a): EPAS1/MYCN, PEG3/GPX7 and THSD4/KCND3. These combinations were validated in the Davicioni data set (b) and the exon array data set (c) with the classification efficiencies indicated.

5 Supplementary Figure 4. Detection of gene expression is comparable for fresh-frozen and paraformaldehyde-fixed material with nCounter

ABFF 1 Kb ladder 100 bp ladder PFA FF

PFA

CD Test Probes RMS Probes PFA Counts PFA Counts PFA

Spike-In Controls RMS Probes (log2) PFA Counts PFA Counts PFA

(a) Agarose gel comparing the DNA extracted from freshly-frozen (FF) and paraformaldehyde (PFA)-fixed rhabdomyosarcoma tumor cell pellets. Note that the DNA from the PFA-fixed cells is smeared, indicating degradation, whereas the DNA from FF cells shows up as a single band. (b) RIN scores and electropherograms indicating the integrity for RNA extracted from FF and PFA- fixed RD cells. (c) nCounter data comparing the gene expression of the FF and PFA-fixed RD cells using a 48 gene test CodeSet (top) and the spike-in positive controls (bottom). (d) nCounter data comparing the gene expression of the FF and PFA-fixed RD cells using our F1/F2 metagene custom CodeSet (normalized data, top; normalized and log2 transformed, bottom, see also Supplemental Table 7).

6 Supplementary Figure 5. Gene expression detected in each case with the Williamson F1/F2 metagene nCounter CodeSet

A 10

2 Normalized Mean Expression (log2)

0 509 2369 2574 4463 6152 6237 6468 10012 10191 10440 12240 12251 13413 15438 22707 24130 IRS 12 IRS 44 IRS 58 IRS 66 IRS 73 IRS 78 IRS 83 IRS 93 IRS 135 IRS 136 12251AP Sample RD FFPE (ERMS) H28 FFPE (ARMSp)

B 9 ) 2 8

2 Normalized Mean Expression (log 1

0 ALK CAD ZIC1 FZD7 FBN2 ASS1 SAE1 GPX7 NRN1 CNR1 PIPOX NELL1 MAGI1 TULP4 ELA2A PTBP2 CPSF1 TRPS1 DDEF1 MFAP2 DAPK1 TNRC9 RBM13 ABCG1 PGBD5 HOXC6 JARID2 HMGA2 NRCAM TFAP2B TAGLN3 GALNT2 SPRED2 PGRMC1 FLJ10159 FLJ10357 KIAA0523 KIAA1018 KIAA1026 LAPTM4B AF070632 EIF4EBP1 AW819521 PAFAH1B3 LOC653127 LOC653754 Gene

C 11

8 R2 = 0.9712 7 y = (-0.0092051) + 1.0054*x

6 12251AP

1 123456789101112 12251

(a) Mean expression and standard deviation of all the genes in the CodeSet for each sample. Red bars indicate RNA extracted from the same sample using two different kits to determine reproducibility. (b) Mean expression and standard deviation of all the samples for each gene in the CodeSet. (c) nCounter data comparing the gene expression of the duplicate samples. 7 SUPPLEMENTARY TABLE 1 Four-gene combinations with ≥ 99% accuracy

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 201121 s at PGRMC1 201639 s at CPSF1 203706 s at FZD7 206446 s at CELA2A/2B 99.0 201121 s at PGRMC1 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 203706 s at FZD7 206446 s at CELA2A/2B 33132 at CPSF1 99.0 201121 s at PGRMC1 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201121 s at PGRMC1 206373 at ZIC1 207076 s at ASS1 218625 at NRN1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 207076 s at ASS1 33132 at CPSF1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219225 at PGBD5 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 218625 at NRN1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 213436 at CNR1 33132 at CPSF1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 214774 x at TOX3 218613 at PSD3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 215108 x at TOX3 218613 at PSD3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 216623 x at TOX3 218613 at PSD3 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 218613 at PSD3 218625 at NRN1 99.0 201121 s at PGRMC1 206446 s at CELA2A/2B 218613 at PSD3 33132 at CPSF1 99.0 201639 s at CPSF1 202715 at CAD 204743 at TAGLN3 221605 s at PIPOX 99.0 201639 s at CPSF1 203139 at DAPK1 206446 s at CELA2A/2B 218613 at PSD3 99.0 201639 s at CPSF1 203184 at FBN2 204743 at TAGLN3 207076 s at ASS1 99.0

8 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 201639 s at CPSF1 203184 at FBN2 206446 s at CELA2A/2B 207076 s at ASS1 99.0 201639 s at CPSF1 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201639 s at CPSF1 203228 at PAFAH1B3 211686 s at RBM13/MAK16 218184 at TULP4 99.0 201639 s at CPSF1 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201639 s at CPSF1 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201639 s at CPSF1 203706 s at FZD7 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 208025 s at HMGA2 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 208767 s at LAPTM4B 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 213832 at KCND3 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 217788 s at GALNT2 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 217946 s at SAE1 99.0 201639 s at CPSF1 204105 s at NRCAM 206446 s at CELA2A/2B 221039 s at ASAP1 99.0 201639 s at CPSF1 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 99.0 201639 s at CPSF1 204743 at TAGLN3 207076 s at ASS1 217946 s at SAE1 99.0 201639 s at CPSF1 204743 at TAGLN3 208212 s at ALK 211686 s at RBM13/MAK16 99.0 201639 s at CPSF1 204743 at TAGLN3 208212 s at ALK 221039 s at ASAP1 99.0 201639 s at CPSF1 204743 at TAGLN3 213170 at GPX7 221605 s at PIPOX 99.0 201639 s at CPSF1 204743 at TAGLN3 218502 s at TRPS1 221605 s at PIPOX 99.0 201639 s at CPSF1 204743 at TAGLN3 218613 at PSD3 221605 s at PIPOX 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 207076 s at ASS1 221039 s at ASAP1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213155 at WSCD1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 218625 at NRN1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221039 s at ASAP1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221605 s at PIPOX 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 212458 at SPRED2 221605 s at PIPOX 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 215108 x at TOX3 218613 at PSD3 99.0 201639 s at CPSF1 206446 s at CELA2A/2B 219060 at WDYHV1 221039 s at ASAP1 99.0 201639 s at CPSF1 206858 s at HOXC6 208212 s at ALK 212458 at SPRED2 99.0 201639 s at CPSF1 208212 s at ALK 218184 at TULP4 218613 at PSD3 99.0 201639 s at CPSF1 213170 at GPX7 218625 at NRN1 221605 s at PIPOX 99.0 201639 s at CPSF1 213478 at KAZN 218502 s at TRPS1 221605 s at PIPOX 99.0 202715 at CAD 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 202715 at CAD 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 202715 at CAD 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 202715 at CAD 204105 s at NRCAM 206446 s at CELA2A/2B 33132 at CPSF1 99.0 202715 at CAD 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 99.0 202715 at CAD 204743 at TAGLN3 212458 at SPRED2 215014 at KCND3 99.0 202715 at CAD 204743 at TAGLN3 213280 at RAP1GAP2 221039 s at ASAP1 99.0 202715 at CAD 206144 at MAGI1 206446 s at CELA2A/2B 221039 s at ASAP1 99.0

9 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 202715 at CAD 206144 at MAGI1 208212 s at ALK 218613 at PSD3 99.0 202715 at CAD 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 202715 at CAD 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 202715 at CAD 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 218625 at NRN1 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 202715 at CAD 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 202715 at CAD 206446 s at CELA2A/2B 218502 s at TRPS1 221039 s at ASAP1 99.0 202715 at CAD 213478 at KAZN 218502 s at TRPS1 221605 s at PIPOX 99.0 203139 at DAPK1 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 206144 at MAGI1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203139 at DAPK1 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 203139 at DAPK1 206446 s at CELA2A/2B 217946 s at SAE1 218613 at PSD3 99.0 203139 at DAPK1 206446 s at CELA2A/2B 218502 s at TRPS1 218613 at PSD3 99.0 203139 at DAPK1 206446 s at CELA2A/2B 218613 at PSD3 33132 at CPSF1 99.0 203184 at FBN2 203228 at PAFAH1B3 204743 at TAGLN3 221039 s at ASAP1 99.0 203184 at FBN2 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 203678 at FAN1 206144 at MAGI1 221605 s at PIPOX 99.0 203184 at FBN2 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 203678 at FAN1 207076 s at ASS1 218625 at NRN1 99.0 203184 at FBN2 203678 at FAN1 208212 s at ALK 221605 s at PIPOX 99.0 203184 at FBN2 203678 at FAN1 218502 s at TRPS1 221605 s at PIPOX 99.0 203184 at FBN2 203678 at FAN1 218613 at PSD3 221605 s at PIPOX 99.0 203184 at FBN2 203678 at FAN1 218625 at NRN1 221605 s at PIPOX 99.0 203184 at FBN2 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 99.0

10 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 203184 at FBN2 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 203184 at FBN2 206446 s at CELA2A/2B 207076 s at ASS1 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 207076 s at ASS1 218502 s at TRPS1 99.0 203184 at FBN2 206446 s at CELA2A/2B 207076 s at ASS1 33132 at CPSF1 99.0 203184 at FBN2 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 203184 at FBN2 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 203184 at FBN2 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 203184 at FBN2 213478 at KAZN 218502 s at TRPS1 221605 s at PIPOX 99.0 203184 at FBN2 213478 at KAZN 218613 at PSD3 221605 s at PIPOX 99.0 203228 at PAFAH1B3 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203228 at PAFAH1B3 204743 at TAGLN3 208212 s at ALK 211686 s at RBM13/MAK16 99.0 203228 at PAFAH1B3 204743 at TAGLN3 212458 at SPRED2 218625 at NRN1 99.0 203228 at PAFAH1B3 204743 at TAGLN3 217946 s at SAE1 221039 s at ASAP1 99.0 203228 at PAFAH1B3 206144 at MAGI1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213155 at WSCD1 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219225 at PGBD5 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 203228 at PAFAH1B3 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203228 at PAFAH1B3 211686 s at RBM13/MAK16 218184 at TULP4 218502 s at TRPS1 99.0 203228 at PAFAH1B3 212458 at SPRED2 218184 at TULP4 218502 s at TRPS1 99.0 203298 s at JARID2 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203298 s at JARID2 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 203298 s at JARID2 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203298 s at JARID2 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 203298 s at JARID2 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0

11 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203298 s at JARID2 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 203417 at MFAP2 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 204743 at TAGLN3 207076 s at ASS1 33132 at CPSF1 99.0 203417 at MFAP2 206144 at MAGI1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 206144 at MAGI1 206446 s at CELA2A/2B 221039 s at ASAP1 99.0 203417 at MFAP2 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203417 at MFAP2 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 99.0 203417 at MFAP2 206446 s at CELA2A/2B 207076 s at ASS1 212458 at SPRED2 99.0 203417 at MFAP2 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203417 at MFAP2 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221605 s at PIPOX 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 213155 at WSCD1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 221605 s at PIPOX 99.0 203417 at MFAP2 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 203417 at MFAP2 213478 at KAZN 218613 at PSD3 221605 s at PIPOX 99.0 203678 at FAN1 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 203678 at FAN1 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 203678 at FAN1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203678 at FAN1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 203678 at FAN1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 218625 at NRN1 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203678 at FAN1 206446 s at CELA2A/2B 212458 at SPRED2 221605 s at PIPOX 99.0 203678 at FAN1 213170 at GPX7 218502 s at TRPS1 221605 s at PIPOX 99.0 203678 at FAN1 213170 at GPX7 218625 at NRN1 221605 s at PIPOX 99.0 203678 at FAN1 213832 at KCND3 218502 s at TRPS1 221605 s at PIPOX 99.0 203678 at FAN1 218502 s at TRPS1 218613 at PSD3 221605 s at PIPOX 99.0

12 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 203706 s at FZD7 204743 at TAGLN3 212458 at SPRED2 221605 s at PIPOX 99.0 203706 s at FZD7 206373 at ZIC1 207076 s at ASS1 218625 at NRN1 99.0 203706 s at FZD7 206373 at ZIC1 212458 at SPRED2 221605 s at PIPOX 99.0 203706 s at FZD7 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 203706 s at FZD7 206446 s at CELA2A/2B 208767 s at LAPTM4B 211686 s at RBM13/MAK16 99.0 203706 s at FZD7 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 203706 s at FZD7 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 203706 s at FZD7 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 217788 s at GALNT2 99.0 203706 s at FZD7 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 217946 s at SAE1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 203706 s at FZD7 206446 s at CELA2A/2B 212458 at SPRED2 221605 s at PIPOX 99.0 204105 s at NRCAM 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 217946 s at SAE1 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 218625 at NRN1 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 204105 s at NRCAM 206446 s at CELA2A/2B 217946 s at SAE1 33132 at CPSF1 99.0 204567 s at ABCG1 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 33132 at CPSF1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 218625 at NRN1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 204567 s at ABCG1 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 204743 at TAGLN3 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 99.0 204743 at TAGLN3 206373 at ZIC1 213170 at GPX7 221605 s at PIPOX 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 99.0

13 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 204743 at TAGLN3 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 204743 at TAGLN3 206446 s at CELA2A/2B 221039 s at ASAP1 221539 at EIF4EBP1 99.0 204743 at TAGLN3 208212 s at ALK 211686 s at RBM13/MAK16 33132 at CPSF1 99.0 204743 at TAGLN3 211686 s at RBM13/MAK16 217946 s at SAE1 218184 at TULP4 99.0 204743 at TAGLN3 212458 at SPRED2 217946 s at SAE1 218184 at TULP4 99.0 204743 at TAGLN3 213170 at GPX7 213436 at CNR1 33132 at CPSF1 99.0 204743 at TAGLN3 217946 s at SAE1 218184 at TULP4 218613 at PSD3 99.0 206089 at NELL1 206373 at ZIC1 212458 at SPRED2 218184 at TULP4 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 206089 at NELL1 206446 s at CELA2A/2B 212458 at SPRED2 33132 at CPSF1 99.0 206089 at NELL1 206446 s at CELA2A/2B 217946 s at SAE1 218613 at PSD3 99.0 206089 at NELL1 206446 s at CELA2A/2B 218613 at PSD3 219060 at WDYHV1 99.0 206144 at MAGI1 206373 at ZIC1 206446 s at CELA2A/2B 221039 s at ASAP1 99.0 206144 at MAGI1 206373 at ZIC1 208212 s at ALK 218613 at PSD3 99.0 206144 at MAGI1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 206144 at MAGI1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 206144 at MAGI1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 206144 at MAGI1 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 206144 at MAGI1 206446 s at CELA2A/2B 218613 at PSD3 219060 at WDYHV1 99.0 206144 at MAGI1 208212 s at ALK 218613 at PSD3 33132 at CPSF1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219225 at PGBD5 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221605 s at PIPOX 99.0 206373 at ZIC1 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 33132 at CPSF1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 99.0

14 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 212458 at SPRED2 221539 at EIF4EBP1 99.0 206373 at ZIC1 206446 s at CELA2A/2B 218613 at PSD3 219225 at PGBD5 99.0 206373 at ZIC1 207076 s at ASS1 211686 s at RBM13/MAK16 218625 at NRN1 99.0 206373 at ZIC1 207076 s at ASS1 213170 at GPX7 218625 at NRN1 99.0 206373 at ZIC1 212458 at SPRED2 218184 at TULP4 218502 s at TRPS1 99.0 206373 at ZIC1 213170 at GPX7 218625 at NRN1 221605 s at PIPOX 99.0 206373 at ZIC1 213478 at KAZN 218502 s at TRPS1 221605 s at PIPOX 99.0 206373 at ZIC1 218184 at TULP4 218613 at PSD3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 207076 s at ASS1 211686 s at RBM13/MAK16 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 208212 s at ALK 212458 at SPRED2 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 211686 s at RBM13/MAK16 213280 at RAP1GAP2 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 211686 s at RBM13/MAK16 219225 at PGBD5 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 213170 at GPX7 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 218625 at NRN1 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 218974 at SOBP 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 206858 s at HOXC6 212458 at SPRED2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 208025 s at HMGA2 211686 s at RBM13/MAK16 99.0 206446 s at CELA2A/2B 207076 s at ASS1 208212 s at ALK 212458 at SPRED2 99.0 206446 s at CELA2A/2B 207076 s at ASS1 208767 s at LAPTM4B 211686 s at RBM13/MAK16 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 213170 at GPX7 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 214774 x at TOX3 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 215108 x at TOX3 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 216623 x at TOX3 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 218613 at PSD3 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 211686 s at RBM13/MAK16 33132 at CPSF1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 218502 s at TRPS1 218613 at PSD3 99.0 206446 s at CELA2A/2B 207076 s at ASS1 218683 at PTBP2 33132 at CPSF1 99.0 206446 s at CELA2A/2B 207076 s at ASS1 221039 s at ASAP1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 208212 s at ALK 212458 at SPRED2 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 211686 s at RBM13/MAK16 213436 at CNR1 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 214774 x at TOX3 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 216623 x at TOX3 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 217788 s at GALNT2 99.0

15 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 218683 at PTBP2 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 218974 at SOBP 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 208025 s at HMGA2 212458 at SPRED2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 208212 s at ALK 208767 s at LAPTM4B 212458 at SPRED2 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 212458 at SPRED2 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 218613 at PSD3 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 219225 at PGBD5 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 208212 s at ALK 211686 s at RBM13/MAK16 33132 at CPSF1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 213170 at GPX7 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 213478 at KAZN 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 213832 at KCND3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 214774 x at TOX3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 215014 at KCND3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 215108 x at TOX3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 216623 x at TOX3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218184 at TULP4 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218613 at PSD3 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218625 at NRN1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218683 at PTBP2 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 218974 at SOBP 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 208212 s at ALK 212458 at SPRED2 33132 at CPSF1 99.0 206446 s at CELA2A/2B 208212 s at ALK 217946 s at SAE1 218613 at PSD3 99.0 206446 s at CELA2A/2B 208212 s at ALK 218613 at PSD3 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 211686 s at RBM13/MAK16 213436 at CNR1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 213170 at GPX7 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 218683 at PTBP2 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 218974 at SOBP 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 212458 at SPRED2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 208767 s at LAPTM4B 218613 at PSD3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 213436 at CNR1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 213478 at KAZN 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 214774 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 215014 at KCND3 99.0

16 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 215108 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 216623 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 218184 at TULP4 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 218613 at PSD3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 218683 at PTBP2 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 218974 at SOBP 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 212458 at SPRED2 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213155 at WSCD1 213280 at RAP1GAP2 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213155 at WSCD1 217946 s at SAE1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213170 at GPX7 221605 s at PIPOX 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 214774 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 215108 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 216623 x at TOX3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 218184 at TULP4 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 218625 at NRN1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 218974 at SOBP 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213280 at RAP1GAP2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 218613 at PSD3 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 218625 at NRN1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 218974 at SOBP 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 213436 at CNR1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 217946 s at SAE1 218625 at NRN1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 217946 s at SAE1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 218613 at PSD3 218625 at NRN1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 218613 at PSD3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 218625 at NRN1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219060 at WDYHV1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219225 at PGBD5 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 219225 at PGBD5 33132 at CPSF1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221039 s at ASAP1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 211686 s at RBM13/MAK16 221605 s at PIPOX 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213155 at WSCD1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213155 at WSCD1 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 214774 x at TOX3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 215108 x at TOX3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 216623 x at TOX3 99.0

17 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 218184 at TULP4 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213170 at GPX7 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213280 at RAP1GAP2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213280 at RAP1GAP2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213436 at CNR1 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 218625 at NRN1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213478 at KAZN 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 214774 x at TOX3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 216623 x at TOX3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 213832 at KCND3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 214774 x at TOX3 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215014 at KCND3 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 215108 x at TOX3 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 217788 s at GALNT2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 221039 s at ASAP1 99.0

18 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206446 s at CELA2A/2B 212458 at SPRED2 216623 x at TOX3 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 217946 s at SAE1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 218625 at NRN1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217788 s at GALNT2 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 218184 at TULP4 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 218502 s at TRPS1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 218613 at PSD3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 218683 at PTBP2 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 217946 s at SAE1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218184 at TULP4 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218184 at TULP4 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 218613 at PSD3 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 221605 s at PIPOX 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218502 s at TRPS1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 218974 at SOBP 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218613 at PSD3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218683 at PTBP2 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 218974 at SOBP 33132 at CPSF1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 220326 s at ARHGEF40 99.0 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 219060 at WDYHV1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 220326 s at ARHGEF40 99.0

19 SUPPLEMENTARY TABLE 1 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 206446 s at CELA2A/2B 212458 at SPRED2 219225 at PGBD5 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 220326 s at ARHGEF40 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 221039 s at ASAP1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 212458 at SPRED2 221605 s at PIPOX 33132 at CPSF1 99.0 206446 s at CELA2A/2B 213155 at WSCD1 218613 at PSD3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 213436 at CNR1 218502 s at TRPS1 33132 at CPSF1 99.0 206446 s at CELA2A/2B 214774 x at TOX3 221039 s at ASAP1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 215108 x at TOX3 218613 at PSD3 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 217788 s at GALNT2 218613 at PSD3 219225 at PGBD5 99.0 206446 s at CELA2A/2B 217788 s at GALNT2 221039 s at ASAP1 221539 at EIF4EBP1 99.0 206446 s at CELA2A/2B 217946 s at SAE1 218613 at PSD3 218625 at NRN1 99.0 206446 s at CELA2A/2B 217946 s at SAE1 218613 at PSD3 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 218502 s at TRPS1 218613 at PSD3 221605 s at PIPOX 99.0 206446 s at CELA2A/2B 218613 at PSD3 218625 at NRN1 219060 at WDYHV1 99.0 206446 s at CELA2A/2B 218613 at PSD3 218974 at SOBP 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 218613 at PSD3 219060 at WDYHV1 219225 at PGBD5 99.0 206446 s at CELA2A/2B 218625 at NRN1 219060 at WDYHV1 221039 s at ASAP1 99.0 206446 s at CELA2A/2B 219060 at WDYHV1 221039 s at ASAP1 33132 at CPSF1 99.0 206858 s at HOXC6 208212 s at ALK 212458 at SPRED2 218625 at NRN1 99.0 206858 s at HOXC6 208212 s at ALK 212458 at SPRED2 33132 at CPSF1 99.0 208212 s at ALK 211686 s at RBM13/MAK16 213170 at GPX7 218184 at TULP4 99.0 208212 s at ALK 212458 at SPRED2 213478 at KAZN 218625 at NRN1 99.0 212458 at SPRED2 217946 s at SAE1 218184 at TULP4 218502 s at TRPS1 99.0 212458 at SPRED2 218184 at TULP4 218502 s at TRPS1 219060 at WDYHV1 99.0 213170 at GPX7 213478 at KAZN 218613 at PSD3 221605 s at PIPOX 99.0 213170 at GPX7 213478 at KAZN 218683 at PTBP2 221605 s at PIPOX 99.0 213478 at KAZN 213832 at KCND3 221605 s at PIPOX 33132 at CPSF1 99.0 213478 at KAZN 215014 at KCND3 221605 s at PIPOX 33132 at CPSF1 99.0 213478 at KAZN 218502 s at TRPS1 218613 at PSD3 221605 s at PIPOX 99.0 213478 at KAZN 218502 s at TRPS1 221605 s at PIPOX 33132 at CPSF1 99.0 218184 at TULP4 218502 s at TRPS1 218613 at PSD3 219060 at WDYHV1 99.0

20 SUPPLEMENTARY TABLE 2 Dyad classifiers from T-test ranking of Williamson data set with ≥ 98% accuracy, applied to Davicioni data *If no classification listed, probe/gene values were not available. Italics: One or both probes not found, symbol(s) queried instead.

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 205150 s at TRIL 221605 s at PIPOX 99.0 100 205731 s at NCOA2 221605 s at PIPOX 99.0 98.6 228904 at HOXB3 221605 s at PIPOX 99.0 97.9 203737 s at PPRC1 206446 s at NA 99.0 94.4 232149 s at NSMAF 226576 at ARHGAP26 99.0 86.7 1554500 a at RGS7 231916 at NOS1 99.0 77.6 1554500 a at RGS7 239132 at NOS1 99.0 77.6 225263 at HS6ST1 239132 at NOS1 99.0 72.7 226421 at AMMECR1 230076 at PITPNM3 99.0 62.2 225292 at COL27A1 221605 s at PIPOX 99.0 ··· 1568957 x at SRGAP2P1 206446 s at NA 99.0 ··· 239466 at LOC344595 210247 at SYN2 99.0 ··· 227083 at B3GALTL 239132 at NOS1 99.0 ··· 235355 at CSRNP3 221605 s at PIPOX 98.0 100 235018 at CSRNP3 221605 s at PIPOX 98.0 100 205151 s at TRIL 221605 s at PIPOX 98.0 100 235017 s at CSRNP3 221605 s at PIPOX 98.0 100 218502 s at TRPS1 214451 at TFAP2B 98.0 99.3 201905 s at CTDSPL 214451 at TFAP2B 98.0 99.3 225676 s at DCAF13 221605 s at PIPOX 98.0 99.3 205848 at GAS2 221605 s at PIPOX 98.0 99.3 206858 s at HOXC6 221605 s at PIPOX 98.0 99.3 219299 at TRMT12 221605 s at PIPOX 98.0 99.3 205372 at PLAG1 221605 s at PIPOX 98.0 99.3 231784 s at DCAF13 221605 s at PIPOX 98.0 99.3 205376 at INPP4B 221605 s at PIPOX 98.0 99.3 212850 s at LRP4 221605 s at PIPOX 98.0 99.3 221802 s at KIAA1598 221605 s at PIPOX 98.0 99.3 222124 at HIF3A 221605 s at PIPOX 98.0 99.3 205696 s at GFRA1 221605 s at PIPOX 98.0 99.3 216840 s at LAMA2 221605 s at PIPOX 98.0 99.3 209893 s at FUT4 221605 s at PIPOX 98.0 99.3 1554500 a at RGS7 221605 s at PIPOX 98.0 99.3 219570 at KIF16B 214451 at TFAP2B 98.0 98.6 203706 s at FZD7 221605 s at PIPOX 98.0 98.6 203355 s at PSD3 221605 s at PIPOX 98.0 98.6 203705 s at FZD7 221605 s at PIPOX 98.0 98.6 213532 at ADAM17 221605 s at PIPOX 98.0 98.6 218502 s at TRPS1 221605 s at PIPOX 98.0 98.6 220233 at NA 221605 s at PIPOX 98.0 98.6 201905 s at CTDSPL 221605 s at PIPOX 98.0 98.6 208842 s at GORASP2 221605 s at PIPOX 98.0 98.6 204015 s at DUSP4 221605 s at PIPOX 98.0 98.6 228837 at TCF4 214451 at TFAP2B 98.0 98.6 212313 at CHMP7 221605 s at PIPOX 98.0 98.6 225168 at FRMD4A 214451 at TFAP2B 98.0 98.6 225168 at FRMD4A 221605 s at PIPOX 98.0 98.6 219837 s at CYTL1 221605 s at PIPOX 98.0 98.6 225167 at FRMD4A 1553394 a at TFAP2B 98.0 98.6 205522 at NA 221605 s at PIPOX 98.0 98.6 205107 s at EF04 221605 s at PIPOX 98.0 98.6 219548 at ZNF16 221605 s at PIPOX 98.0 98.6 217511 at KAZALD1 221605 s at PIPOX 98.0 98.6 209262 s at NR2F6 214451 at TFAP2B 98.0 98.6 201904 s at CTDSPL 214451 at TFAP2B 98.0 98.6 219319 at HIF3A 221605 s at PIPOX 98.0 98.6 205732 s at NCOA2 221605 s at PIPOX 98.0 98.6 220941 s at C21orf91 214451 at TFAP2B 98.0 98.6 219774 at CCDC93 221605 s at PIPOX 98.0 98.6 212256 at GALNT10 214451 at TFAP2B 98.0 98.6 218070 s at GMPPA 221605 s at PIPOX 98.0 98.6 205116 at LAMA2 221605 s at PIPOX 98.0 98.6 217299 s at NBN 221605 s at PIPOX 98.0 98.6 224894 at YAP1 221605 s at PIPOX 98.0 98.6

21 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 241122 s at MUSK 221605 s at PIPOX 98.0 98.6 218284 at SMAD3 221605 s at PIPOX 98.0 98.6 204983 s at GPC4 221605 s at PIPOX 98.0 98.6 218932 at ZNHIT6 221605 s at PIPOX 98.0 98.6 219973 at ARSJ 221605 s at PIPOX 98.0 98.6 222654 at IMPAD1 221605 s at PIPOX 98.0 98.6 1562234 a at 0V3 221605 s at PIPOX 98.0 98.6 203184 at FBN2 214451 at TFAP2B 98.0 97.9 212458 at SPRED2 221605 s at PIPOX 98.0 97.9 222199 s at BIN3 221605 s at PIPOX 98.0 97.9 202680 at GTF2E2 214451 at TFAP2B 98.0 97.9 220911 s at NYNRIN 214451 at TFAP2B 98.0 97.9 211686 s at MAK16 221605 s at PIPOX 98.0 97.9 203269 at NSMAF 221605 s at PIPOX 98.0 97.9 201984 s at EGFR 214451 at TFAP2B 98.0 97.9 212867 at NCOA2 221605 s at PIPOX 98.0 97.9 219231 at TGS1 221605 s at PIPOX 98.0 97.9 223023 at BET1L 221605 s at PIPOX 98.0 97.9 203941 at INTS9 221605 s at PIPOX 98.0 97.9 218665 at FZD4 221605 s at PIPOX 98.0 97.9 204087 s at SLC5A6 221605 s at PIPOX 98.0 97.9 207118 s at NA 221605 s at PIPOX 98.0 97.9 225583 at UXS1 221605 s at PIPOX 98.0 97.9 218905 at INTS8 214451 at TFAP2B 98.0 97.9 218905 at INTS8 221605 s at PIPOX 98.0 97.9 208674 x at DDOST 221605 s at PIPOX 98.0 97.9 225010 at CCDC6 214451 at TFAP2B 98.0 97.9 209892 at FUT4 221605 s at PIPOX 98.0 97.9 218135 at ERGIC2 214451 at TFAP2B 98.0 97.9 202758 s at RFXANK 214451 at TFAP2B 98.0 97.9 221094 s at ELP3 221605 s at PIPOX 98.0 97.9 215690 x at GPAA1 221605 s at PIPOX 98.0 97.9 219124 at TTI2 221605 s at PIPOX 98.0 97.9 226974 at NEDD4L 221605 s at PIPOX 98.0 97.9 202134 s at WWTR1 221605 s at PIPOX 98.0 97.9 211126 s at CSRP2 214451 at TFAP2B 98.0 97.9 204086 at PRAME 221605 s at PIPOX 98.0 97.9 200076 s at KXD1 214451 at TFAP2B 98.0 97.9 209406 at BAG2 214451 at TFAP2B 98.0 97.9 209406 at BAG2 221605 s at PIPOX 98.0 97.9 208060 at PAX7 221605 s at PIPOX 98.0 97.9 218337 at FAM160B2 221605 s at PIPOX 98.0 97.9 211432 s at TYRO3 221605 s at PIPOX 98.0 97.9 208639 x at PDIA6 221605 s at PIPOX 98.0 97.9 211958 at IGFBP5 214451 at TFAP2B 98.0 97.9 208658 at PDIA4 221605 s at PIPOX 98.0 97.9 213243 at VPS13B 214451 at TFAP2B 98.0 97.9 205228 at RBMS2 221605 s at PIPOX 98.0 97.9 205667 at WRN 221605 s at PIPOX 98.0 97.9 218823 s at KCTD9 1553394 a at TFAP2B 98.0 97.9 218823 s at KCTD9 221605 s at PIPOX 98.0 97.9 213848 at DUSP7 214451 at TFAP2B 98.0 97.9 201652 at COPS5 1553394 a at TFAP2B 98.0 97.9 201719 s at EPB41L2 221605 s at PIPOX 98.0 97.9 222400 s at ADI1 221605 s at PIPOX 98.0 97.9 220014 at PRR16 221605 s at PIPOX 98.0 97.9 203669 s at DGAT1 221605 s at PIPOX 98.0 97.9 208843 s at GORASP2 221605 s at PIPOX 98.0 97.9 214394 x at EEF1D 221605 s at PIPOX 98.0 97.9 222454 s at PARVA 221605 s at PIPOX 98.0 97.9 206194 at NA 221605 s at PIPOX 98.0 97.9 210419 at BARX2 221605 s at PIPOX 98.0 97.9 213150 at HOXA10 221605 s at PIPOX 98.0 97.9 203261 at DCTN6 221605 s at PIPOX 98.0 97.9 207030 s at CSRP2 214451 at TFAP2B 98.0 97.9 214003 x at RPS20 221605 s at PIPOX 98.0 97.9 204068 at STK3 221605 s at PIPOX 98.0 97.9 207668 x at PDIA6 221605 s at PIPOX 98.0 97.9

22 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 220474 at SLC25A21 221605 s at PIPOX 98.0 97.9 221786 at C6orf120 214451 at TFAP2B 98.0 97.9 218926 at MYNN 221605 s at PIPOX 98.0 97.9 215418 at PARVA 214451 at TFAP2B 98.0 97.9 91952 at DCAF15 214451 at TFAP2B 98.0 97.9 205113 at NEFM 221605 s at PIPOX 98.0 97.9 235311 at FKBP14 221605 s at PIPOX 98.0 97.9 216241 s at TCEA1 221605 s at PIPOX 98.0 97.2 202680 at GTF2E2 221605 s at PIPOX 98.0 97.2 210023 s at PCGF1 221605 s at PIPOX 98.0 97.2 207812 s at GORASP2 221605 s at PIPOX 98.0 97.2 210296 s at PEX2 221605 s at PIPOX 98.0 97.2 209517 s at ASH2L 221605 s at PIPOX 98.0 97.2 1558290 a at PVT1 221605 s at PIPOX 98.0 97.2 225010 at CCDC6 221605 s at PIPOX 98.0 97.2 202670 at MAP2K1 221605 s at PIPOX 98.0 97.2 218135 at ERGIC2 221605 s at PIPOX 98.0 97.2 213891 s at TCF4 221605 s at PIPOX 98.0 97.2 208713 at HNRNPUL1 221605 s at PIPOX 98.0 97.2 209567 at RRS1 221605 s at PIPOX 98.0 97.2 212885 at MPHOSPH10 221605 s at PIPOX 98.0 97.2 223216 x at ZNF395 221605 s at PIPOX 98.0 97.2 202906 s at NBN 221605 s at PIPOX 98.0 97.2 242887 at KCMF1 221605 s at PIPOX 98.0 97.2 218059 at ZNF706 221605 s at PIPOX 98.0 97.2 222335 at NA 221605 s at PIPOX 98.0 97.2 201652 at COPS5 221605 s at PIPOX 98.0 97.2 202824 s at TCEB1 221605 s at PIPOX 98.0 97.2 213391 at DPY19L4 221605 s at PIPOX 98.0 97.2 219312 s at ZBTB10 221605 s at PIPOX 98.0 97.2 220967 s at ZNF696 221605 s at PIPOX 98.0 97.2 232983 s at SERGEF 221605 s at PIPOX 98.0 97.2 202174 s at PCM1 221605 s at PIPOX 98.0 97.2 200949 x at RPS20 221605 s at PIPOX 98.0 97.2 1554155 at MCPH1 221605 s at PIPOX 98.0 97.2 214626 s at GA0B 221605 s at PIPOX 98.0 97.2 221786 at C6orf120 221605 s at PIPOX 98.0 97.2 212466 at SPRED2 221605 s at PIPOX 98.0 97.2 200608 s at RAD21 221605 s at PIPOX 98.0 97.2 209227 at TUSC3 221605 s at PIPOX 98.0 97.2 202447 at DECR1 221605 s at PIPOX 98.0 97.2 214937 x at PCM1 221605 s at PIPOX 98.0 97.2 224791 at ASAP1 221605 s at PIPOX 98.0 96.5 202313 at PPP2R2A 221605 s at PIPOX 98.0 96.5 213891 s at TCF4 205889 s at JAKMIP2 98.0 96.5 217899 at TMEM214 221605 s at PIPOX 98.0 96.5 200062 s at RPL30 221605 s at PIPOX 98.0 96.5 213564 x at LDHB 221605 s at PIPOX 98.0 96.5 209384 at PROSC 221605 s at PIPOX 98.0 96.5 220890 s at DDX47 221605 s at PIPOX 98.0 96.5 201030 x at LDHB 221605 s at PIPOX 98.0 96.5 217092 x at RPL7 221605 s at PIPOX 98.0 96.5 1555889 a at CRTAP 221605 s at PIPOX 98.0 95.8 221959 at FAM110B 213157 s at WSCD1 98.0 95.8 217792 at SNX5 206446 s at NA 98.0 95.1 212458 at SPRED2 206446 s at NA 98.0 94.4 201984 s at EGFR 213436 at CNR1 98.0 94.4 202423 at KAT6A 206446 s at NA 98.0 94.4 217946 s at SAE1 206446 s at NA 98.0 94.4 205731 s at NCOA2 213436 at CNR1 98.0 94.4 202744 at SLC20A2 206446 s at NA 98.0 94.4 213243 at VPS13B 213436 at CNR1 98.0 94.4 210829 s at SSBP2 206446 s at NA 98.0 93.7 203184 at FBN2 1556606 at 0V2 98.0 92.3 202905 x at NBN 226576 at ARHGAP26 98.0 92.3 201764 at TMEM106C 206447 at NA 98.0 92.3 203184 at FBN2 240911 at NOS1 98.0 91.6 203184 at FBN2 239132 at NOS1 98.0 91.6

23 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 232083 at KIF16B 204570 at COX7A1 98.0 91.6 203426 s at IGFBP5 206128 at ADRA2C 98.0 91.6 213342 at YAP1 226576 at ARHGAP26 98.0 91.6 203184 at FBN2 230498 at MCHR1 98.0 90.9 232083 at KIF16B 204824 at ENDOG 98.0 89.5 211737 x at PTN 240911 at NOS1 98.0 89.5 209465 x at PTN 240911 at NOS1 98.0 89.5 209466 x at PTN 240911 at NOS1 98.0 89.5 210023 s at PCGF1 206447 at NA 98.0 89.5 1552658 a at 0V3 1556606 at 0V2 98.0 89.5 204823 at 0V3 1556606 at 0V2 98.0 89.5 212385 at TCF4 226576 at ARHGAP26 98.0 89.5 1562234 a at 0V3 1556606 at 0V2 98.0 89.5 203355 s at PSD3 209693 at ASTN2 98.0 88.8 209883 at GLT25D2 240911 at NOS1 98.0 88.8 218665 at FZD4 240911 at NOS1 98.0 88.8 209516 at SMYD5 206447 at NA 98.0 88.8 201367 s at ZFP36L2 226576 at ARHGAP26 98.0 88.8 213532 at ADAM17 226576 at ARHGAP26 98.0 88.1 241700 at ZFHX4 240911 at NOS1 98.0 88.1 205848 at GAS2 240911 at NOS1 98.0 88.1 205848 at GAS2 239132 at NOS1 98.0 88.1 219779 at ZFHX4 240911 at NOS1 98.0 88.1 224206 x at MYNN 226576 at ARHGAP26 98.0 88.1 216306 x at PTBP1 226576 at ARHGAP26 98.0 87.4 226421 at AMMECR1 226576 at ARHGAP26 98.0 87.4 204036 at LPAR1 240911 at NOS1 98.0 87.4 204037 at LPAR1 240911 at NOS1 98.0 87.4 210296 s at PEX2 226576 at ARHGAP26 98.0 87.4 204038 s at LPAR1 240911 at NOS1 98.0 87.4 204976 s at AMMECR1 226576 at ARHGAP26 98.0 87.4 218465 at TMEM33 226576 at ARHGAP26 98.0 87.4 226331 at BBX 226576 at ARHGAP26 98.0 87.4 210257 x at CUL4B 226576 at ARHGAP26 98.0 87.4 232083 at KIF16B 240911 at NOS1 98.0 86.7 216241 s at TCEA1 226576 at ARHGAP26 98.0 86.7 219884 at LHX6 240911 at NOS1 98.0 86.7 204716 at CCDC6 226576 at ARHGAP26 98.0 86.7 201069 at MMP2 240911 at NOS1 98.0 86.7 203706 s at FZD7 240911 at NOS1 98.0 86.0 203706 s at FZD7 239132 at NOS1 98.0 86.0 203705 s at FZD7 240911 at NOS1 98.0 86.0 203705 s at FZD7 239132 at NOS1 98.0 86.0 235355 at CSRNP3 240911 at NOS1 98.0 86.0 235355 at CSRNP3 231916 at NOS1 98.0 86.0 235355 at CSRNP3 239132 at NOS1 98.0 86.0 235018 at CSRNP3 240911 at NOS1 98.0 86.0 235018 at CSRNP3 231916 at NOS1 98.0 86.0 235018 at CSRNP3 239132 at NOS1 98.0 86.0 203669 s at DGAT1 206447 at NA 98.0 86 205020 s at ARL4A 240911 at NOS1 98.0 86.0 235017 s at CSRNP3 240911 at NOS1 98.0 86.0 235017 s at CSRNP3 231916 at NOS1 98.0 86.0 235017 s at CSRNP3 239132 at NOS1 98.0 86.0 218816 at LRRC1 1556606 at 0V2 98.0 85.3 222651 s at TRPS1 240911 at NOS1 98.0 85.3 222651 s at TRPS1 239132 at NOS1 98.0 85.3 218502 s at TRPS1 240911 at NOS1 98.0 85.3 218502 s at TRPS1 239132 at NOS1 98.0 85.3 224218 s at TRPS1 240911 at NOS1 98.0 85.3 201787 at FBLN1 240911 at NOS1 98.0 85.3 235012 at LRCH1 226576 at ARHGAP26 98.0 85.3 204235 s at GULP1 240911 at NOS1 98.0 85.3 226795 at LRCH1 226576 at ARHGAP26 98.0 85.3 208025 s at HMGA2 240911 at NOS1 98.0 85.3 208025 s at HMGA2 1556606 at 0V2 98.0 85.3 208025 s at HMGA2 239132 at NOS1 98.0 85.3 215913 s at GULP1 240911 at NOS1 98.0 85.3

24 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 218839 at HEY1 240911 at NOS1 98.0 85.3 216705 s at ADA 240911 at NOS1 98.0 85.3 204237 at GULP1 240911 at NOS1 98.0 85.3 204237 at GULP1 239132 at NOS1 98.0 85.3 204639 at ADA 240911 at NOS1 98.0 85.3 234351 x at TRPS1 240911 at NOS1 98.0 85.3 44783 s at HEY1 240911 at NOS1 98.0 85.3 202747 s at ITM2A 1556606 at 0V2 98.0 85.3 207790 at LRRC1 1556606 at 0V2 98.0 85.3 1554500 a at RGS7 1556606 at 0V2 98.0 85.3 214721 x at CDC42EP4 240911 at NOS1 98.0 84.6 224999 at EGFR 240911 at NOS1 98.0 84.6 224999 at EGFR 239132 at NOS1 98.0 84.6 218974 at SOBP 240911 at NOS1 98.0 84.6 218062 x at CDC42EP4 240911 at NOS1 98.0 84.6 201984 s at EGFR 240911 at NOS1 98.0 84.6 201984 s at EGFR 239132 at NOS1 98.0 84.6 219894 at MAGEL2 1556606 at 0V2 98.0 84.6 209568 s at RGL1 240911 at NOS1 98.0 84.6 229034 at SOBP 240911 at NOS1 98.0 84.6 205372 at PLAG1 240911 at NOS1 98.0 84.6 205372 at PLAG1 231916 at NOS1 98.0 84.6 205372 at PLAG1 239132 at NOS1 98.0 84.6 202747 s at ITM2A 240911 at NOS1 98.0 84.6 202747 s at ITM2A 239132 at NOS1 98.0 84.6 202746 at ITM2A 240911 at NOS1 98.0 84.6 202345 s at FABP5 240911 at NOS1 98.0 84.6 201983 s at EGFR 240911 at NOS1 98.0 84.6 202956 at ARFGEF1 1556606 at 0V2 98.0 84.6 224999 at EGFR 1556606 at 0V2 98.0 83.9 220911 s at NYNRIN 240911 at NOS1 98.0 83.9 220911 s at NYNRIN 239132 at NOS1 98.0 83.9 218959 at HOXC10 240911 at NOS1 98.0 83.9 218959 at HOXC10 239132 at NOS1 98.0 83.9 201984 s at EGFR 1556606 at 0V2 98.0 83.9 221539 at EIF4EBP1 240911 at NOS1 98.0 83.9 221539 at EIF4EBP1 239132 at NOS1 98.0 83.9 201939 at PLK2 240911 at NOS1 98.0 83.9 204015 s at DUSP4 240911 at NOS1 98.0 83.9 204015 s at DUSP4 239132 at NOS1 98.0 83.9 201618 x at GPAA1 206447 at NA 98.0 83.9 226034 at DUSP4 240911 at NOS1 98.0 83.9 226034 at DUSP4 239132 at NOS1 98.0 83.9 217511 at KAZALD1 1556606 at 0V2 98.0 83.9 206858 s at HOXC6 240911 at NOS1 98.0 83.9 206858 s at HOXC6 239132 at NOS1 98.0 83.9 219319 at HIF3A 240911 at NOS1 98.0 83.9 219319 at HIF3A 231916 at NOS1 98.0 83.9 219319 at HIF3A 239132 at NOS1 98.0 83.9 215690 x at GPAA1 206447 at NA 98.0 83.9 204014 at DUSP4 240911 at NOS1 98.0 83.9 204014 at DUSP4 239132 at NOS1 98.0 83.9 211060 x at GPAA1 206447 at NA 98.0 83.9 202800 at SLC1A3 240911 at NOS1 98.0 83.9 221019 s at COLEC12 240911 at NOS1 98.0 83.9 222124 at HIF3A 240911 at NOS1 98.0 83.9 222124 at HIF3A 231916 at NOS1 98.0 83.9 222124 at HIF3A 239132 at NOS1 98.0 83.9 207069 s at SMAD6 240911 at NOS1 98.0 83.9 218816 at LRRC1 240911 at NOS1 98.0 83.2 218816 at LRRC1 231916 at NOS1 98.0 83.2 218816 at LRRC1 239132 at NOS1 98.0 83.2 1555889 a at CRTAP 229053 at SYT17 98.0 83.2 208882 s at UBR5 1556606 at 0V2 98.0 83.2 235355 at CSRNP3 230076 at PITPNM3 98.0 83.2 1556638 at PAX7 240911 at NOS1 98.0 83.2 1556638 at PAX7 239132 at NOS1 98.0 83.2 208884 s at UBR5 1556606 at 0V2 98.0 83.2

25 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 206767 at RBMS3 240911 at NOS1 98.0 83.2 235570 at RBMS3 240911 at NOS1 98.0 83.2 235570 at RBMS3 239132 at NOS1 98.0 83.2 219863 at HERC5 240911 at NOS1 98.0 83.2 208060 at PAX7 240911 at NOS1 98.0 83.2 208060 at PAX7 239132 at NOS1 98.0 83.2 242137 at RBMS3 240911 at NOS1 98.0 83.2 65718 at GPR124 1556606 at 0V2 98.0 83.2 207790 at LRRC1 240911 at NOS1 98.0 83.2 207790 at LRRC1 239132 at NOS1 98.0 83.2 220014 at PRR16 1556606 at 0V2 98.0 83.2 238447 at RBMS3 240911 at NOS1 98.0 83.2 208883 at UBR5 1556606 at 0V2 98.0 83.2 221000 s at KAZALD1 240911 at NOS1 98.0 82.5 1568598 at KAZALD1 240911 at NOS1 98.0 82.5 212445 s at NEDD4L 240911 at NOS1 98.0 82.5 221582 at HIST3H2A 240911 at NOS1 98.0 82.5 201206 s at RRBP1 240911 at NOS1 98.0 82.5 217511 at KAZALD1 240911 at NOS1 98.0 82.5 212448 at NEDD4L 240911 at NOS1 98.0 82.5 212448 at NEDD4L 239132 at NOS1 98.0 82.5 210380 s at CAC01G 1556606 at 0V2 98.0 82.5 1569025 s at FAM13A 240911 at NOS1 98.0 82.5 1569025 s at FAM13A 231916 at NOS1 98.0 82.5 1569025 s at FAM13A 239132 at NOS1 98.0 82.5 226974 at NEDD4L 240911 at NOS1 98.0 82.5 218337 at FAM160B2 1556606 at 0V2 98.0 82.5 205151 s at TRIL 1556606 at 0V2 98.0 82.5 201204 s at RRBP1 240911 at NOS1 98.0 82.5 201203 s at RRBP1 240911 at NOS1 98.0 82.5 205150 s at TRIL 1556606 at 0V2 98.0 82.5 207144 s at CITED1 230498 at MCHR1 98.0 82.5 1569024 at FAM13A 240911 at NOS1 98.0 82.5 217047 s at FAM13A 240911 at NOS1 98.0 82.5 205542 at STEAP1 240911 at NOS1 98.0 82.5 213342 at YAP1 240911 at NOS1 98.0 81.8 211121 s at DOK1 240911 at NOS1 98.0 81.8 224895 at YAP1 240911 at NOS1 98.0 81.8 218777 at REEP4 240911 at NOS1 98.0 81.8 206745 at HOXC11 240911 at NOS1 98.0 81.8 221810 at RAB15 1556606 at 0V2 98.0 81.8 219550 at ROBO3 240911 at NOS1 98.0 81.8 205376 at INPP4B 240911 at NOS1 98.0 81.8 205376 at INPP4B 239132 at NOS1 98.0 81.8 59697 at RAB15 1556606 at 0V2 98.0 81.8 204239 s at N0T 240911 at NOS1 98.0 81.8 204239 s at N0T 239132 at NOS1 98.0 81.8 212850 s at LRP4 231916 at NOS1 98.0 81.8 212850 s at LRP4 239132 at NOS1 98.0 81.8 216835 s at DOK1 240911 at NOS1 98.0 81.8 224894 at YAP1 240911 at NOS1 98.0 81.8 224894 at YAP1 239132 at NOS1 98.0 81.8 205667 at WRN 1556606 at 0V2 98.0 81.8 201719 s at EPB41L2 1556606 at 0V2 98.0 81.8 207144 s at CITED1 240911 at NOS1 98.0 81.8 207144 s at CITED1 239132 at NOS1 98.0 81.8 204301 at KBTBD11 240911 at NOS1 98.0 81.8 204301 at KBTBD11 231916 at NOS1 98.0 81.8 204301 at KBTBD11 239132 at NOS1 98.0 81.8 235046 at INPP4B 240911 at NOS1 98.0 81.8 235046 at INPP4B 239132 at NOS1 98.0 81.8 209509 s at DPAGT1 1556606 at 0V2 98.0 81.8 203355 s at PSD3 240911 at NOS1 98.0 81.1 203355 s at PSD3 239132 at NOS1 98.0 81.1 224796 at ASAP1 1556606 at 0V2 98.0 81.1 205698 s at MAP2K6 240911 at NOS1 98.0 81.1 218613 at PSD3 230498 at MCHR1 98.0 81.1 218613 at PSD3 240911 at NOS1 98.0 81.1

26 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 218613 at PSD3 239132 at NOS1 98.0 81.1 224791 at ASAP1 1556606 at 0V2 98.0 81.1 224790 at ASAP1 1556606 at 0V2 98.0 81.1 201905 s at CTDSPL 240911 at NOS1 98.0 81.1 201905 s at CTDSPL 1556606 at 0V2 98.0 81.1 201905 s at CTDSPL 231916 at NOS1 98.0 81.1 201905 s at CTDSPL 239132 at NOS1 98.0 81.1 211686 s at MAK16 1556606 at 0V2 98.0 81.1 204442 x at LTBP4 240911 at NOS1 98.0 81.1 204442 x at LTBP4 239132 at NOS1 98.0 81.1 219231 at TGS1 1556606 at 0V2 98.0 81.1 202786 at STK39 240911 at NOS1 98.0 81.1 202786 at STK39 231916 at NOS1 98.0 81.1 202786 at STK39 239132 at NOS1 98.0 81.1 218689 at FANCF 240911 at NOS1 98.0 81.1 218689 at FANCF 239132 at NOS1 98.0 81.1 221959 at FAM110B 240911 at NOS1 98.0 81.1 221959 at FAM110B 239132 at NOS1 98.0 81.1 202479 s at TRIB2 240911 at NOS1 98.0 81.1 222713 s at FANCF 240911 at NOS1 98.0 81.1 201904 s at CTDSPL 240911 at NOS1 98.0 81.1 201904 s at CTDSPL 1556606 at 0V2 98.0 81.1 201904 s at CTDSPL 239132 at NOS1 98.0 81.1 204163 at EMILIN1 240911 at NOS1 98.0 81.1 202478 at TRIB2 240911 at NOS1 98.0 81.1 212665 at TIPARP 240911 at NOS1 98.0 81.1 201870 at TOMM34 240911 at NOS1 98.0 81.1 210380 s at CAC01G 240911 at NOS1 98.0 81.1 210380 s at CAC01G 231916 at NOS1 98.0 81.1 210380 s at CAC01G 239132 at NOS1 98.0 81.1 202701 at BMP1 240911 at NOS1 98.0 81.1 219682 s at TBX3 240911 at NOS1 98.0 81.1 201906 s at CTDSPL 240911 at NOS1 98.0 81.1 202906 s at NBN 1556606 at 0V2 98.0 81.1 222917 s at TBX3 240911 at NOS1 98.0 81.1 210628 x at LTBP4 240911 at NOS1 98.0 81.1 213176 s at LTBP4 240911 at NOS1 98.0 81.1 213176 s at LTBP4 239132 at NOS1 98.0 81.1 207595 s at BMP1 240911 at NOS1 98.0 81.1 228790 at FAM110B 240911 at NOS1 98.0 81.1 203449 s at TERF1 1556606 at 0V2 98.0 81.1 207144 s at CITED1 1556606 at 0V2 98.0 81.1 212377 s at NOTCH2 205946 at VIPR2 98.0 81.1 225544 at TBX3 240911 at NOS1 98.0 81.1 218162 at OLFML3 240911 at NOS1 98.0 81.1 211802 x at CAC01G 240911 at NOS1 98.0 81.1 203355 s at PSD3 230076 at PITPNM3 98.0 80.4 207424 at MYF5 240911 at NOS1 98.0 80.4 211518 s at BMP4 240911 at NOS1 98.0 80.4 212360 at AMPD2 240911 at NOS1 98.0 80.4 1552658 a at 0V3 240911 at NOS1 98.0 80.4 1552658 a at 0V3 231916 at NOS1 98.0 80.4 1552658 a at 0V3 239132 at NOS1 98.0 80.4 219511 s at SNCAIP 240911 at NOS1 98.0 80.4 201995 at EXT1 240911 at NOS1 98.0 80.4 201995 at EXT1 239132 at NOS1 98.0 80.4 204823 at 0V3 240911 at NOS1 98.0 80.4 204823 at 0V3 231916 at NOS1 98.0 80.4 204823 at 0V3 239132 at NOS1 98.0 80.4 237833 s at SNCAIP 240911 at NOS1 98.0 80.4 237833 s at SNCAIP 239132 at NOS1 98.0 80.4 206805 at SEMA3A 240911 at NOS1 98.0 80.4 221810 at RAB15 240911 at NOS1 98.0 80.4 221810 at RAB15 231916 at NOS1 98.0 80.4 221810 at RAB15 239132 at NOS1 98.0 80.4 59697 at RAB15 240911 at NOS1 98.0 80.4 59697 at RAB15 231916 at NOS1 98.0 80.4 59697 at RAB15 239132 at NOS1 98.0 80.4

27 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 230183 at EXT1 240911 at NOS1 98.0 80.4 222454 s at PARVA 1556606 at 0V2 98.0 80.4 213113 s at SLC43A3 240911 at NOS1 98.0 80.4 219060 at WDYHV1 1556606 at 0V2 98.0 80.4 209983 s at NRXN2 1556606 at 0V2 98.0 80.4 202443 x at NOTCH2 205946 at VIPR2 98.0 80.4 215418 at PARVA 1556606 at 0V2 98.0 80.4 1562234 a at 0V3 240911 at NOS1 98.0 80.4 1562234 a at 0V3 231916 at NOS1 98.0 80.4 1562234 a at 0V3 239132 at NOS1 98.0 80.4 216466 at 0V3 240911 at NOS1 98.0 80.4 216466 at 0V3 231916 at NOS1 98.0 80.4 216466 at 0V3 239132 at NOS1 98.0 80.4 212867 at NCOA2 240911 at NOS1 98.0 79.7 212867 at NCOA2 231916 at NOS1 98.0 79.7 212867 at NCOA2 239132 at NOS1 98.0 79.7 223125 s at C1orf21 240911 at NOS1 98.0 79.7 218689 at FANCF 230076 at PITPNM3 98.0 79.7 212313 at CHMP7 239132 at NOS1 98.0 79.7 210023 s at PCGF1 1556606 at 0V2 98.0 79.7 205732 s at NCOA2 240911 at NOS1 98.0 79.7 205732 s at NCOA2 231916 at NOS1 98.0 79.7 205732 s at NCOA2 239132 at NOS1 98.0 79.7 221814 at GPR124 240911 at NOS1 98.0 79.7 213479 at NPTX2 240911 at NOS1 98.0 79.7 213891 s at TCF4 1556606 at 0V2 98.0 79.7 205731 s at NCOA2 240911 at NOS1 98.0 79.7 205731 s at NCOA2 231916 at NOS1 98.0 79.7 205731 s at NCOA2 239132 at NOS1 98.0 79.7 211126 s at CSRP2 1556606 at 0V2 98.0 79.7 223126 s at C1orf21 240911 at NOS1 98.0 79.7 205116 at LAMA2 240911 at NOS1 98.0 79.7 205116 at LAMA2 239132 at NOS1 98.0 79.7 65718 at GPR124 240911 at NOS1 98.0 79.7 221272 s at C1orf21 240911 at NOS1 98.0 79.7 202561 at TNKS 1556606 at 0V2 98.0 79.7 214394 x at EEF1D 240911 at NOS1 98.0 79.7 213519 s at LAMA2 240911 at NOS1 98.0 79.7 213519 s at LAMA2 239132 at NOS1 98.0 79.7 216840 s at LAMA2 240911 at NOS1 98.0 79.7 216840 s at LAMA2 239132 at NOS1 98.0 79.7 201287 s at SDC1 240911 at NOS1 98.0 79.7 203113 s at EEF1D 240911 at NOS1 98.0 79.7 209708 at MOXD1 240911 at NOS1 98.0 79.7 201286 at SDC1 240911 at NOS1 98.0 79.7 232148 at NSMAF 1556606 at 0V2 98.0 79.7 202680 at GTF2E2 1556606 at 0V2 98.0 79.0 217788 s at GALNT2 240911 at NOS1 98.0 79.0 223991 s at GALNT2 240911 at NOS1 98.0 79.0 202786 at STK39 230076 at PITPNM3 98.0 79.0 217787 s at GALNT2 240911 at NOS1 98.0 79.0 201368 at ZFP36L2 240911 at NOS1 98.0 79.0 219894 at MAGEL2 240911 at NOS1 98.0 79.0 219894 at MAGEL2 239132 at NOS1 98.0 79.0 203488 at LPHN1 240911 at NOS1 98.0 79.0 218695 at EXOSC4 240911 at NOS1 98.0 79.0 218245 at TSKU 240911 at NOS1 98.0 79.0 47560 at LPHN1 240911 at NOS1 98.0 79.0 220941 s at C21orf91 240911 at NOS1 98.0 79.0 1552337 s at HOXD4 240911 at NOS1 98.0 79.0 1552337 s at HOXD4 239132 at NOS1 98.0 79.0 203534 at LSM1 1556606 at 0V2 98.0 79.0 201369 s at ZFP36L2 240911 at NOS1 98.0 79.0 219145 at LPHN1 240911 at NOS1 98.0 79.0 201764 at TMEM106C 240911 at NOS1 98.0 79.0 58696 at EXOSC4 240911 at NOS1 98.0 79.0 204724 s at COL9A3 240911 at NOS1 98.0 79.0 218826 at SLC35F2 240911 at NOS1 98.0 79.0

28 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 219215 s at SLC39A4 240911 at NOS1 98.0 79.0 214394 x at EEF1D 1556606 at 0V2 98.0 79.0 201367 s at ZFP36L2 240911 at NOS1 98.0 79.0 202824 s at TCEB1 1556606 at 0V2 98.0 79.0 220967 s at ZNF696 1556606 at 0V2 98.0 79.0 202788 at MAPKAPK3 240911 at NOS1 98.0 79.0 218125 s at CCDC25 1556606 at 0V2 98.0 79.0 226109 at C21orf91 240911 at NOS1 98.0 79.0 223614 at MMP16 240911 at NOS1 98.0 79.0 91684 g at EXOSC4 240911 at NOS1 98.0 79.0 209227 at TUSC3 1556606 at 0V2 98.0 79.0 235801 at TUSC3 1556606 at 0V2 98.0 79.0 217999 s at PHLDA1 240911 at NOS1 98.0 78.3 202925 s at PLAGL2 240911 at NOS1 98.0 78.3 202925 s at PLAGL2 239132 at NOS1 98.0 78.3 203426 s at IGFBP5 240911 at NOS1 98.0 78.3 206303 s at NUDT4 240911 at NOS1 98.0 78.3 217998 at PHLDA1 240911 at NOS1 98.0 78.3 202894 at EPHB4 240911 at NOS1 98.0 78.3 203737 s at PPRC1 1556606 at 0V2 98.0 78.3 202145 at LY6E 240911 at NOS1 98.0 78.3 208767 s at LAPTM4B 240911 at NOS1 98.0 78.3 208767 s at LAPTM4B 239132 at NOS1 98.0 78.3 212256 at GALNT10 240911 at NOS1 98.0 78.3 212256 at GALNT10 239132 at NOS1 98.0 78.3 201985 at KIAA0196 1556606 at 0V2 98.0 78.3 1555997 s at IGFBP5 240911 at NOS1 98.0 78.3 208029 s at LAPTM4B 240911 at NOS1 98.0 78.3 208029 s at LAPTM4B 239132 at NOS1 98.0 78.3 203425 s at IGFBP5 240911 at NOS1 98.0 78.3 1554679 a at LAPTM4B 240911 at NOS1 98.0 78.3 1554679 a at LAPTM4B 239132 at NOS1 98.0 78.3 214039 s at LAPTM4B 240911 at NOS1 98.0 78.3 214039 s at LAPTM4B 239132 at NOS1 98.0 78.3 218070 s at GMPPA 1556606 at 0V2 98.0 78.3 202924 s at PLAGL2 240911 at NOS1 98.0 78.3 225842 at PHLDA1 240911 at NOS1 98.0 78.3 218000 s at PHLDA1 240911 at NOS1 98.0 78.3 217997 at PHLDA1 240911 at NOS1 98.0 78.3 217997 at PHLDA1 239132 at NOS1 98.0 78.3 211958 at IGFBP5 240911 at NOS1 98.0 78.3 203424 s at IGFBP5 240911 at NOS1 98.0 78.3 207357 s at GALNT10 240911 at NOS1 98.0 78.3 221836 s at TRAPPC9 240911 at NOS1 98.0 78.3 209545 s at RIPK2 240911 at NOS1 98.0 78.3 203071 at SEMA3B 240911 at NOS1 98.0 78.3 203669 s at DGAT1 1556606 at 0V2 98.0 78.3 205031 at EFNB3 240911 at NOS1 98.0 78.3 207144 s at CITED1 230076 at PITPNM3 98.0 78.3 218454 at PLBD1 240911 at NOS1 98.0 78.3 218125 s at CCDC25 240911 at NOS1 98.0 78.3 227376 at GLI3 240911 at NOS1 98.0 78.3 204679 at KCNK1 240911 at NOS1 98.0 78.3 204068 at STK3 1556606 at 0V2 98.0 78.3 219973 at ARSJ 240911 at NOS1 98.0 78.3 219973 at ARSJ 239132 at NOS1 98.0 78.3 209544 at RIPK2 240911 at NOS1 98.0 78.3 209544 at RIPK2 239132 at NOS1 98.0 78.3 210762 s at DLC1 240911 at NOS1 98.0 78.3 212183 at NUDT4 240911 at NOS1 98.0 78.3 224822 at DLC1 240911 at NOS1 98.0 78.3 216680 s at EPHB4 240911 at NOS1 98.0 78.3 217996 at PHLDA1 240911 at NOS1 98.0 78.3 221234 s at BACH2 240911 at NOS1 98.0 78.3 201121 s at PGRMC1 240911 at NOS1 98.0 77.6 201121 s at PGRMC1 239132 at NOS1 98.0 77.6 1555889 a at CRTAP 1556606 at 0V2 98.0 77.6 229228 at CREB5 240911 at NOS1 98.0 77.6

29 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 202907 s at NBN 240911 at NOS1 98.0 77.6 202907 s at NBN 239132 at NOS1 98.0 77.6 202905 x at NBN 240911 at NOS1 98.0 77.6 202925 s at PLAGL2 1556606 at 0V2 98.0 77.6 201120 s at PGRMC1 240911 at NOS1 98.0 77.6 203417 at MFAP2 240911 at NOS1 98.0 77.6 232555 at CREB5 240911 at NOS1 98.0 77.6 212188 at KCTD12 240911 at NOS1 98.0 77.6 209247 s at ABCF2 240911 at NOS1 98.0 77.6 209247 s at ABCF2 239132 at NOS1 98.0 77.6 203119 at CCDC86 240911 at NOS1 98.0 77.6 203119 at CCDC86 239132 at NOS1 98.0 77.6 201639 s at CPSF1 1556606 at 0V2 98.0 77.6 33132 at CPSF1 1556606 at 0V2 98.0 77.6 212248 at MTDH 1556606 at 0V2 98.0 77.6 203870 at USP46 1556606 at 0V2 98.0 77.6 202134 s at WWTR1 240911 at NOS1 98.0 77.6 202134 s at WWTR1 231916 at NOS1 98.0 77.6 202134 s at WWTR1 239132 at NOS1 98.0 77.6 212814 at AHCYL2 240911 at NOS1 98.0 77.6 212356 at KHNYN 240911 at NOS1 98.0 77.6 203534 at LSM1 240911 at NOS1 98.0 77.6 203534 at LSM1 239132 at NOS1 98.0 77.6 212355 at KHNYN 240911 at NOS1 98.0 77.6 202734 at TRIP10 240911 at NOS1 98.0 77.6 202906 s at NBN 240911 at NOS1 98.0 77.6 202906 s at NBN 239132 at NOS1 98.0 77.6 205931 s at CREB5 240911 at NOS1 98.0 77.6 217299 s at NBN 240911 at NOS1 98.0 77.6 219832 s at HOXC13 240911 at NOS1 98.0 77.6 207622 s at ABCF2 240911 at NOS1 98.0 77.6 214433 s at SELENBP1 240911 at NOS1 98.0 77.6 205031 at EFNB3 1556606 at 0V2 98.0 77.6 212192 at KCTD12 240911 at NOS1 98.0 77.6 218900 at CNNM4 240911 at NOS1 98.0 77.6 215672 s at AHCYL2 240911 at NOS1 98.0 77.6 203451 at LDB1 240911 at NOS1 98.0 77.6 35160 at LDB1 240911 at NOS1 98.0 77.6 209544 at RIPK2 1556606 at 0V2 98.0 77.6 216836 s at ERBB2 240911 at NOS1 98.0 77.6 203431 s at ARHGAP32 240911 at NOS1 98.0 77.6 203431 s at ARHGAP32 239132 at NOS1 98.0 77.6 210791 s at ARHGAP32 240911 at NOS1 98.0 77.6 210791 s at ARHGAP32 239132 at NOS1 98.0 77.6 219427 at FAT4 240911 at NOS1 98.0 77.6 1554500 a at RGS7 240911 at NOS1 98.0 77.6 222199 s at BIN3 240911 at NOS1 98.0 76.9 222199 s at BIN3 239132 at NOS1 98.0 76.9 236270 at NFATC4 240911 at NOS1 98.0 76.9 236270 at NFATC4 239132 at NOS1 98.0 76.9 222853 at FLRT3 240911 at NOS1 98.0 76.9 204404 at SLC12A2 240911 at NOS1 98.0 76.9 208916 at SLC1A5 240911 at NOS1 98.0 76.9 219250 s at FLRT3 240911 at NOS1 98.0 76.9 209517 s at ASH2L 1556606 at 0V2 98.0 76.9 201772 at AZIN1 1556606 at 0V2 98.0 76.9 213345 at NFATC4 240911 at NOS1 98.0 76.9 213345 at NFATC4 239132 at NOS1 98.0 76.9 208712 at CCND1 240911 at NOS1 98.0 76.9 215690 x at GPAA1 1556606 at 0V2 98.0 76.9 202814 s at HEXIM1 240911 at NOS1 98.0 76.9 1555358 a at ENTPD4 240911 at NOS1 98.0 76.9 1555358 a at ENTPD4 231916 at NOS1 98.0 76.9 1555358 a at ENTPD4 239132 at NOS1 98.0 76.9 204086 at PRAME 240911 at NOS1 98.0 76.9 204086 at PRAME 239132 at NOS1 98.0 76.9 223216 x at ZNF395 1556606 at 0V2 98.0 76.9 219039 at SEMA4C 240911 at NOS1 98.0 76.9

30 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 218337 at FAM160B2 240911 at NOS1 98.0 76.9 218337 at FAM160B2 239132 at NOS1 98.0 76.9 236896 at ZIC1 240911 at NOS1 98.0 76.9 236896 at ZIC1 239132 at NOS1 98.0 76.9 225835 at SLC12A2 240911 at NOS1 98.0 76.9 213147 at HOXA10 240911 at NOS1 98.0 76.9 219685 at TMEM35 240911 at NOS1 98.0 76.9 219685 at TMEM35 239132 at NOS1 98.0 76.9 208711 s at CCND1 240911 at NOS1 98.0 76.9 204040 at RNF144A 240911 at NOS1 98.0 76.9 213150 at HOXA10 240911 at NOS1 98.0 76.9 213150 at HOXA10 239132 at NOS1 98.0 76.9 202815 s at HEXIM1 240911 at NOS1 98.0 76.9 46665 at SEMA4C 240911 at NOS1 98.0 76.9 206373 at ZIC1 240911 at NOS1 98.0 76.9 216176 at HCRP1 240911 at NOS1 98.0 76.9 216174 at HCRP1 240911 at NOS1 98.0 76.9 213045 at MAST3 240911 at NOS1 98.0 76.9 227550 at GFRA1 240911 at NOS1 98.0 76.2 227550 at GFRA1 239132 at NOS1 98.0 76.2 223023 at BET1L 240911 at NOS1 98.0 76.2 223023 at BET1L 239132 at NOS1 98.0 76.2 204087 s at SLC5A6 223715 at BRSK2 98.0 76.2 210296 s at PEX2 1556606 at 0V2 98.0 76.2 202313 at PPP2R2A 1556606 at 0V2 98.0 76.2 219299 at TRMT12 1556606 at 0V2 98.0 76.2 219103 at ASAP3 240911 at NOS1 98.0 76.2 221094 s at ELP3 1556606 at 0V2 98.0 76.2 222236 s at ASAP3 240911 at NOS1 98.0 76.2 230163 at GFRA1 240911 at NOS1 98.0 76.2 230163 at GFRA1 231916 at NOS1 98.0 76.2 230163 at GFRA1 239132 at NOS1 98.0 76.2 205047 s at ASNS 240911 at NOS1 98.0 76.2 209253 at SORBS3 240911 at NOS1 98.0 76.2 208060 at PAX7 1556606 at 0V2 98.0 76.2 212793 at DAAM2 240911 at NOS1 98.0 76.2 222692 s at FNDC3B 240911 at NOS1 98.0 76.2 205204 at NMB 240911 at NOS1 98.0 76.2 208113 x at PABPC3 1556606 at 0V2 98.0 76.2 223842 s at SCARA3 240911 at NOS1 98.0 76.2 223842 s at SCARA3 239132 at NOS1 98.0 76.2 219416 at SCARA3 240911 at NOS1 98.0 76.2 221845 s at CLPB 240911 at NOS1 98.0 76.2 205150 s at TRIL 230076 at PITPNM3 98.0 76.2 221802 s at KIAA1598 240911 at NOS1 98.0 76.2 221802 s at KIAA1598 239132 at NOS1 98.0 76.2 213848 at DUSP7 240911 at NOS1 98.0 76.2 204214 s at RAB32 240911 at NOS1 98.0 76.2 206217 at EDA 240911 at NOS1 98.0 76.2 217809 at BZW2 240911 at NOS1 98.0 76.2 219215 s at SLC39A4 1556606 at 0V2 98.0 76.2 205696 s at GFRA1 240911 at NOS1 98.0 76.2 205696 s at GFRA1 231916 at NOS1 98.0 76.2 205696 s at GFRA1 239132 at NOS1 98.0 76.2 210419 at BARX2 1556606 at 0V2 98.0 76.2 225032 at FNDC3B 240911 at NOS1 98.0 76.2 212377 s at NOTCH2 240911 at NOS1 98.0 76.2 200717 x at RPL7 1556606 at 0V2 98.0 76.2 202443 x at NOTCH2 240911 at NOS1 98.0 76.2 228013 at PPP2R2A 1556606 at 0V2 98.0 76.2 220470 at BET1L 240911 at NOS1 98.0 76.2 220470 at BET1L 239132 at NOS1 98.0 76.2 217092 x at RPL7 1556606 at 0V2 98.0 76.2 225168 at FRMD4A 240911 at NOS1 98.0 75.5 225168 at FRMD4A 239132 at NOS1 98.0 75.5 219837 s at CYTL1 240911 at NOS1 98.0 75.5 219837 s at CYTL1 239132 at NOS1 98.0 75.5 225167 at FRMD4A 240911 at NOS1 98.0 75.5

31 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 225167 at FRMD4A 239132 at NOS1 98.0 75.5 201618 x at GPAA1 240911 at NOS1 98.0 75.5 219548 at ZNF16 1556606 at 0V2 98.0 75.5 209262 s at NR2F6 1556606 at 0V2 98.0 75.5 227911 at ARHGAP28 240911 at NOS1 98.0 75.5 227911 at ARHGAP28 239132 at NOS1 98.0 75.5 224206 x at MYNN 1556606 at 0V2 98.0 75.5 201827 at SMARCD2 240911 at NOS1 98.0 75.5 215690 x at GPAA1 240911 at NOS1 98.0 75.5 208713 at HNRNPUL1 1556606 at 0V2 98.0 75.5 211060 x at GPAA1 240911 at NOS1 98.0 75.5 209567 at RRS1 240911 at NOS1 98.0 75.5 209567 at RRS1 239132 at NOS1 98.0 75.5 200617 at MLEC 1556606 at 0V2 98.0 75.5 218070 s at GMPPA 240911 at NOS1 98.0 75.5 218070 s at GMPPA 239132 at NOS1 98.0 75.5 235459 at RNF41 240911 at NOS1 98.0 75.5 201566 x at ID2 240911 at NOS1 98.0 75.5 201565 s at ID2 240911 at NOS1 98.0 75.5 201433 s at PTDSS1 1556606 at 0V2 98.0 75.5 209592 s at DCAF7 240911 at NOS1 98.0 75.5 205228 at RBMS2 240911 at NOS1 98.0 75.5 228504 at SCN7A 240911 at NOS1 98.0 75.5 225163 at FRMD4A 240911 at NOS1 98.0 75.5 225163 at FRMD4A 239132 at NOS1 98.0 75.5 202875 s at PBX2 240911 at NOS1 98.0 75.5 212096 s at MTUS1 240911 at NOS1 98.0 75.5 220134 x at FAM176B 240911 at NOS1 98.0 75.5 209983 s at NRXN2 240911 at NOS1 98.0 75.5 209983 s at NRXN2 239132 at NOS1 98.0 75.5 208704 x at APLP2 240911 at NOS1 98.0 75.5 208702 x at APLP2 240911 at NOS1 98.0 75.5 214875 x at APLP2 240911 at NOS1 98.0 75.5 220382 s at ARHGAP28 240911 at NOS1 98.0 75.5 220382 s at ARHGAP28 239132 at NOS1 98.0 75.5 208476 s at FRMD4A 240911 at NOS1 98.0 75.5 218926 at MYNN 1556606 at 0V2 98.0 75.5 208248 x at APLP2 240911 at NOS1 98.0 75.5 203910 at ARHGAP29 240911 at NOS1 98.0 75.5 209129 at TRIP6 240911 at NOS1 98.0 74.8 209441 at RHOBTB2 240911 at NOS1 98.0 74.8 209441 at RHOBTB2 239132 at NOS1 98.0 74.8 1558290 a at PVT1 240911 at NOS1 98.0 74.8 1558290 a at PVT1 239132 at NOS1 98.0 74.8 219299 at TRMT12 240911 at NOS1 98.0 74.8 219299 at TRMT12 231916 at NOS1 98.0 74.8 219299 at TRMT12 239132 at NOS1 98.0 74.8 222543 at DERL1 1556606 at 0V2 98.0 74.8 201126 s at MGAT1 240911 at NOS1 98.0 74.8 208546 x at HIST1H2BH 240911 at NOS1 98.0 74.8 205151 s at TRIL 240911 at NOS1 98.0 74.8 205151 s at TRIL 239132 at NOS1 98.0 74.8 205150 s at TRIL 240911 at NOS1 98.0 74.8 205150 s at TRIL 239132 at NOS1 98.0 74.8 221802 s at KIAA1598 230076 at PITPNM3 98.0 74.8 219312 s at ZBTB10 1556606 at 0V2 98.0 74.8 206601 s at HOXD3 240911 at NOS1 98.0 74.8 206601 s at HOXD3 239132 at NOS1 98.0 74.8 232983 s at SERGEF 240911 at NOS1 98.0 74.8 1554586 a at RHOBTB2 240911 at NOS1 98.0 74.8 210257 x at CUL4B 240911 at NOS1 98.0 74.8 200599 s at HSP90B1 239132 at NOS1 98.0 74.8 228904 at HOXB3 240911 at NOS1 98.0 74.1 228904 at HOXB3 239132 at NOS1 98.0 74.1 235012 at LRCH1 240911 at NOS1 98.0 74.1 203941 at INTS9 240911 at NOS1 98.0 74.1 203941 at INTS9 231916 at NOS1 98.0 74.1 203941 at INTS9 239132 at NOS1 98.0 74.1

32 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 226795 at LRCH1 240911 at NOS1 98.0 74.1 205107 s at EF04 240911 at NOS1 98.0 74.1 209325 s at RGS16 240911 at NOS1 98.0 74.1 218135 at ERGIC2 1556606 at 0V2 98.0 74.1 205732 s at NCOA2 230076 at PITPNM3 98.0 74.1 221094 s at ELP3 240911 at NOS1 98.0 74.1 221094 s at ELP3 239132 at NOS1 98.0 74.1 206147 x at SCML2 240911 at NOS1 98.0 74.1 206147 x at SCML2 239132 at NOS1 98.0 74.1 203643 at ERF 240911 at NOS1 98.0 74.1 209324 s at RGS16 240911 at NOS1 98.0 74.1 209324 s at RGS16 239132 at NOS1 98.0 74.1 201639 s at CPSF1 239132 at NOS1 98.0 74.1 33132 at CPSF1 240911 at NOS1 98.0 74.1 33132 at CPSF1 239132 at NOS1 98.0 74.1 205731 s at NCOA2 230076 at PITPNM3 98.0 74.1 209516 at SMYD5 1556606 at 0V2 98.0 74.1 204073 s at C11orf9 240911 at NOS1 98.0 74.1 222454 s at PARVA 240911 at NOS1 98.0 74.1 209218 at SQLE 1556606 at 0V2 98.0 74.1 209817 at PPP3CB 1556606 at 0V2 98.0 74.1 202218 s at FADS2 240911 at NOS1 98.0 74.1 215418 at PARVA 239132 at NOS1 98.0 74.1 200608 s at RAD21 1556606 at 0V2 98.0 74.1 207524 at ST7 239132 at NOS1 98.0 74.1 212611 at DTX4 240911 at NOS1 98.0 74.1 208414 s at HOXB3 240911 at NOS1 98.0 74.1 201644 at TSTA3 240911 at NOS1 98.0 73.4 201644 at TSTA3 239132 at NOS1 98.0 73.4 201398 s at TRAM1 240911 at NOS1 98.0 73.4 36936 at TSTA3 240911 at NOS1 98.0 73.4 36936 at TSTA3 1556606 at 0V2 98.0 73.4 36936 at TSTA3 239132 at NOS1 98.0 73.4 208675 s at DDOST 240911 at NOS1 98.0 73.4 208674 x at DDOST 240911 at NOS1 98.0 73.4 1558290 a at PVT1 1556606 at 0V2 98.0 73.4 209892 at FUT4 240911 at NOS1 98.0 73.4 209892 at FUT4 239132 at NOS1 98.0 73.4 229377 at GRTP1 1556606 at 0V2 98.0 73.4 208361 s at POLR3D 240911 at NOS1 98.0 73.4 222701 s at CHCHD7 240911 at NOS1 98.0 73.4 208642 s at XRCC5 240911 at NOS1 98.0 73.4 211432 s at TYRO3 240911 at NOS1 98.0 73.4 211432 s at TYRO3 239132 at NOS1 98.0 73.4 218426 s at RNF216 240911 at NOS1 98.0 73.4 229281 at NPAS3 240911 at NOS1 98.0 73.4 229281 at NPAS3 239132 at NOS1 98.0 73.4 201399 s at TRAM1 240911 at NOS1 98.0 73.4 231382 at FGF18 240911 at NOS1 98.0 73.4 231382 at FGF18 239132 at NOS1 98.0 73.4 209516 at SMYD5 240911 at NOS1 98.0 73.4 209516 at SMYD5 239132 at NOS1 98.0 73.4 241122 s at MUSK 240911 at NOS1 98.0 73.4 241122 s at MUSK 239132 at NOS1 98.0 73.4 201652 at COPS5 1556606 at 0V2 98.0 73.4 218031 s at FOXN3 240911 at NOS1 98.0 73.4 202561 at TNKS 240911 at NOS1 98.0 73.4 202561 at TNKS 231916 at NOS1 98.0 73.4 202561 at TNKS 239132 at NOS1 98.0 73.4 230412 at NPAS3 231916 at NOS1 98.0 73.4 230412 at NPAS3 239132 at NOS1 98.0 73.4 219922 s at LTBP3 240911 at NOS1 98.0 73.4 219922 s at LTBP3 239132 at NOS1 98.0 73.4 209817 at PPP3CB 240911 at NOS1 98.0 73.4 209817 at PPP3CB 231916 at NOS1 98.0 73.4 209817 at PPP3CB 239132 at NOS1 98.0 73.4 222494 at FOXN3 240911 at NOS1 98.0 73.4 222494 at FOXN3 239132 at NOS1 98.0 73.4

33 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 205022 s at FOXN3 240911 at NOS1 98.0 73.4 220316 at NPAS3 240911 at NOS1 98.0 73.4 220316 at NPAS3 239132 at NOS1 98.0 73.4 215084 s at LRRC42 239132 at NOS1 98.0 73.4 212823 s at PLEKHG3 240911 at NOS1 98.0 73.4 212823 s at PLEKHG3 239132 at NOS1 98.0 73.4 218425 at RNF216 240911 at NOS1 98.0 73.4 220474 at SLC25A21 240911 at NOS1 98.0 73.4 219904 at ZSCAN5A 240911 at NOS1 98.0 73.4 209893 s at FUT4 240911 at NOS1 98.0 73.4 209893 s at FUT4 239132 at NOS1 98.0 73.4 203114 at SSSCA1 240911 at NOS1 98.0 73.4 201592 at EIF3H 1556606 at 0V2 98.0 73.4 212369 at ZNF384 240911 at NOS1 98.0 73.4 211029 x at FGF18 240911 at NOS1 98.0 73.4 224076 s at WHSC1L1 240911 at NOS1 98.0 73.4 224076 s at WHSC1L1 239132 at NOS1 98.0 73.4 215259 s at CADM4 240911 at NOS1 98.0 73.4 204897 at PTGER4 240911 at NOS1 98.0 73.4 1555889 a at CRTAP 240911 at NOS1 98.0 72.7 202680 at GTF2E2 240911 at NOS1 98.0 72.7 202680 at GTF2E2 230076 at PITPNM3 98.0 72.7 202680 at GTF2E2 231916 at NOS1 98.0 72.7 202680 at GTF2E2 239132 at NOS1 98.0 72.7 1554464 a at CRTAP 240911 at NOS1 98.0 72.7 203941 at INTS9 230076 at PITPNM3 98.0 72.7 228837 at TCF4 240911 at NOS1 98.0 72.7 228837 at TCF4 239132 at NOS1 98.0 72.7 210023 s at PCGF1 239132 at NOS1 98.0 72.7 218905 at INTS8 240911 at NOS1 98.0 72.7 218905 at INTS8 231916 at NOS1 98.0 72.7 218905 at INTS8 239132 at NOS1 98.0 72.7 210022 at PCGF1 240911 at NOS1 98.0 72.7 222757 s at ZAK 240911 at NOS1 98.0 72.7 222757 s at ZAK 239132 at NOS1 98.0 72.7 213891 s at TCF4 240911 at NOS1 98.0 72.7 213891 s at TCF4 239132 at NOS1 98.0 72.7 212385 at TCF4 240911 at NOS1 98.0 72.7 205375 at MDFI 240911 at NOS1 98.0 72.7 201480 s at SUPT5H 240911 at NOS1 98.0 72.7 201718 s at EPB41L2 240911 at NOS1 98.0 72.7 225263 at HS6ST1 240911 at NOS1 98.0 72.7 225263 at HS6ST1 231916 at NOS1 98.0 72.7 212713 at MFAP4 240911 at NOS1 98.0 72.7 209453 at SLC9A1 240911 at NOS1 98.0 72.7 209384 at PROSC 240911 at NOS1 98.0 72.7 209384 at PROSC 239132 at NOS1 98.0 72.7 212386 at TCF4 240911 at NOS1 98.0 72.7 213243 at VPS13B 240911 at NOS1 98.0 72.7 213243 at VPS13B 231916 at NOS1 98.0 72.7 213243 at VPS13B 239132 at NOS1 98.0 72.7 218629 at SMO 240911 at NOS1 98.0 72.7 220890 s at DDX47 1556606 at 0V2 98.0 72.7 201719 s at EPB41L2 240911 at NOS1 98.0 72.7 220014 at PRR16 240911 at NOS1 98.0 72.7 220014 at PRR16 239132 at NOS1 98.0 72.7 212382 at TCF4 240911 at NOS1 98.0 72.7 210419 at BARX2 240911 at NOS1 98.0 72.7 210419 at BARX2 239132 at NOS1 98.0 72.7 218284 at SMAD3 240911 at NOS1 98.0 72.7 218284 at SMAD3 239132 at NOS1 98.0 72.7 200773 x at PTMA 240911 at NOS1 98.0 72.7 200051 at SART1 240911 at NOS1 98.0 72.7 218955 at BRF2 240911 at NOS1 98.0 72.7 218955 at BRF2 239132 at NOS1 98.0 72.7 1556429 a at WDR67 1556606 at 0V2 98.0 72.7 202212 at PES1 240911 at NOS1 98.0 72.7 221586 s at E2F5 240911 at NOS1 98.0 72.7

34 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 221586 s at E2F5 231916 at NOS1 98.0 72.7 221586 s at E2F5 239132 at NOS1 98.0 72.7 218954 s at BRF2 240911 at NOS1 98.0 72.7 201937 s at DNPEP 240911 at NOS1 98.0 72.7 218833 at ZAK 240911 at NOS1 98.0 72.7 205113 at NEFM 240911 at NOS1 98.0 72.7 205113 at NEFM 239132 at NOS1 98.0 72.7 209227 at TUSC3 230076 at PITPNM3 98.0 72.7 235801 at TUSC3 230076 at PITPNM3 98.0 72.7 202440 s at ST5 240911 at NOS1 98.0 72.7 209385 s at PROSC 240911 at NOS1 98.0 72.7 208989 s at KDM2A 240911 at NOS1 98.0 72.7 201380 at CRTAP 240911 at NOS1 98.0 72.7 221039 s at ASAP1 240911 at NOS1 98.0 72.0 221039 s at ASAP1 231916 at NOS1 98.0 72.0 221039 s at ASAP1 239132 at NOS1 98.0 72.0 224796 at ASAP1 240911 at NOS1 98.0 72.0 224796 at ASAP1 239132 at NOS1 98.0 72.0 213532 at ADAM17 1556606 at 0V2 98.0 72.0 224791 at ASAP1 240911 at NOS1 98.0 72.0 224791 at ASAP1 231916 at NOS1 98.0 72.0 224791 at ASAP1 239132 at NOS1 98.0 72.0 224790 at ASAP1 240911 at NOS1 98.0 72.0 224790 at ASAP1 239132 at NOS1 98.0 72.0 221020 s at SLC25A32 240911 at NOS1 98.0 72.0 221020 s at SLC25A32 239132 at NOS1 98.0 72.0 204087 s at SLC5A6 240911 at NOS1 98.0 72.0 204087 s at SLC5A6 239132 at NOS1 98.0 72.0 225010 at CCDC6 240911 at NOS1 98.0 72.0 225010 at CCDC6 231916 at NOS1 98.0 72.0 225010 at CCDC6 239132 at NOS1 98.0 72.0 209262 s at NR2F6 240911 at NOS1 98.0 72.0 209262 s at NR2F6 239132 at NOS1 98.0 72.0 202313 at PPP2R2A 240911 at NOS1 98.0 72.0 202313 at PPP2R2A 239132 at NOS1 98.0 72.0 201772 at AZIN1 240911 at NOS1 98.0 72.0 201772 at AZIN1 239132 at NOS1 98.0 72.0 209928 s at MSC 240911 at NOS1 98.0 72.0 204716 at CCDC6 240911 at NOS1 98.0 72.0 204716 at CCDC6 239132 at NOS1 98.0 72.0 203870 at USP46 240911 at NOS1 98.0 72.0 203870 at USP46 239132 at NOS1 98.0 72.0 206739 at HOXC5 240911 at NOS1 98.0 72.0 206739 at HOXC5 239132 at NOS1 98.0 72.0 211126 s at CSRP2 240911 at NOS1 98.0 72.0 211126 s at CSRP2 239132 at NOS1 98.0 72.0 219755 at CBX8 240911 at NOS1 98.0 72.0 221004 s at ITM2C 240911 at NOS1 98.0 72.0 205135 s at NUFIP1 240911 at NOS1 98.0 72.0 203088 at FBLN5 240911 at NOS1 98.0 72.0 219825 at CYP26B1 240911 at NOS1 98.0 72.0 235205 at OXR1 1556606 at 0V2 98.0 72.0 203449 s at TERF1 240911 at NOS1 98.0 72.0 203449 s at TERF1 231916 at NOS1 98.0 72.0 203449 s at TERF1 239132 at NOS1 98.0 72.0 212461 at AZIN1 240911 at NOS1 98.0 72.0 212461 at AZIN1 239132 at NOS1 98.0 72.0 219197 s at SCUBE2 240911 at NOS1 98.0 72.0 201605 x at CNN2 240911 at NOS1 98.0 72.0 220967 s at ZNF696 240911 at NOS1 98.0 72.0 220967 s at ZNF696 231916 at NOS1 98.0 72.0 220967 s at ZNF696 239132 at NOS1 98.0 72.0 204983 s at GPC4 240911 at NOS1 98.0 72.0 204983 s at GPC4 239132 at NOS1 98.0 72.0 207030 s at CSRP2 240911 at NOS1 98.0 72.0 207030 s at CSRP2 239132 at NOS1 98.0 72.0 1554155 at MCPH1 1556606 at 0V2 98.0 72.0 218932 at ZNHIT6 1556606 at 0V2 98.0 72.0

35 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 208523 x at HIST1H2BI 240911 at NOS1 98.0 72.0 228013 at PPP2R2A 240911 at NOS1 98.0 72.0 228013 at PPP2R2A 239132 at NOS1 98.0 72.0 201874 at MPZL1 240911 at NOS1 98.0 72.0 213072 at CYHR1 240911 at NOS1 98.0 72.0 209227 at TUSC3 240911 at NOS1 98.0 72.0 209227 at TUSC3 239132 at NOS1 98.0 72.0 235801 at TUSC3 240911 at NOS1 98.0 72.0 235801 at TUSC3 239132 at NOS1 98.0 72.0 218905 at INTS8 230076 at PITPNM3 98.0 71.3 227911 at ARHGAP28 1556606 at 0V2 98.0 71.3 214873 at LRP5L 240911 at NOS1 98.0 71.3 202744 at SLC20A2 240911 at NOS1 98.0 71.3 213170 at GPX7 1556606 at 0V2 98.0 71.3 222411 s at SSR3 240911 at NOS1 98.0 71.3 213243 at VPS13B 1556606 at 0V2 98.0 71.3 209043 at PAPSS1 240911 at NOS1 98.0 71.3 219418 at NHEJ1 240911 at NOS1 98.0 71.3 219418 at NHEJ1 239132 at NOS1 98.0 71.3 242887 at KCMF1 1556606 at 0V2 98.0 71.3 226331 at BBX 240911 at NOS1 98.0 71.3 202174 s at PCM1 240911 at NOS1 98.0 71.3 202174 s at PCM1 239132 at NOS1 98.0 71.3 221579 s at NUDT3 240911 at NOS1 98.0 71.3 1557331 at POLR1B 240911 at NOS1 98.0 71.3 1557331 at POLR1B 231916 at NOS1 98.0 71.3 1557331 at POLR1B 239132 at NOS1 98.0 71.3 220382 s at ARHGAP28 1556606 at 0V2 98.0 71.3 221786 at C6orf120 1556606 at 0V2 98.0 71.3 214937 x at PCM1 240911 at NOS1 98.0 71.3 214937 x at PCM1 239132 at NOS1 98.0 71.3 212458 at SPRED2 240911 at NOS1 98.0 70.6 212458 at SPRED2 230076 at PITPNM3 98.0 70.6 212458 at SPRED2 231916 at NOS1 98.0 70.6 212458 at SPRED2 239132 at NOS1 98.0 70.6 219675 s at UXS1 240911 at NOS1 98.0 70.6 225583 at UXS1 240911 at NOS1 98.0 70.6 225583 at UXS1 230076 at PITPNM3 98.0 70.6 225583 at UXS1 239132 at NOS1 98.0 70.6 219548 at ZNF16 240911 at NOS1 98.0 70.6 219548 at ZNF16 239132 at NOS1 98.0 70.6 228882 at TUB 240911 at NOS1 98.0 70.6 222543 at DERL1 240911 at NOS1 98.0 70.6 222543 at DERL1 231916 at NOS1 98.0 70.6 222543 at DERL1 239132 at NOS1 98.0 70.6 219402 s at DERL1 240911 at NOS1 98.0 70.6 225263 at HS6ST1 1556606 at 0V2 98.0 70.6 202639 s at RANBP3 240911 at NOS1 98.0 70.6 205667 at WRN 231916 at NOS1 98.0 70.6 205667 at WRN 239132 at NOS1 98.0 70.6 206746 at BFSP1 240911 at NOS1 98.0 70.6 202955 s at ARFGEF1 240911 at NOS1 98.0 70.6 202955 s at ARFGEF1 239132 at NOS1 98.0 70.6 203261 at DCTN6 1556606 at 0V2 98.0 70.6 218172 s at DERL1 240911 at NOS1 98.0 70.6 218172 s at DERL1 239132 at NOS1 98.0 70.6 201512 s at TOMM70A 240911 at NOS1 98.0 70.6 216266 s at ARFGEF1 240911 at NOS1 98.0 70.6 216266 s at ARFGEF1 239132 at NOS1 98.0 70.6 226463 at ATP6V1C1 240911 at NOS1 98.0 70.6 209428 s at ZFPL1 240911 at NOS1 98.0 70.6 212466 at SPRED2 240911 at NOS1 98.0 70.6 212466 at SPRED2 239132 at NOS1 98.0 70.6 202956 at ARFGEF1 240911 at NOS1 98.0 70.6 202956 at ARFGEF1 231916 at NOS1 98.0 70.6 202956 at ARFGEF1 239132 at NOS1 98.0 70.6 1554153 a at PHF21A 240911 at NOS1 98.0 70.6 219997 s at COPS7B 240911 at NOS1 98.0 70.6

36 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 211686 s at MAK16 240911 at NOS1 98.0 69.9 211686 s at MAK16 231916 at NOS1 98.0 69.9 211686 s at MAK16 239132 at NOS1 98.0 69.9 200824 at GSTP1 240911 at NOS1 98.0 69.9 208882 s at UBR5 240911 at NOS1 98.0 69.9 208882 s at UBR5 231916 at NOS1 98.0 69.9 208882 s at UBR5 239132 at NOS1 98.0 69.9 208884 s at UBR5 240911 at NOS1 98.0 69.9 208884 s at UBR5 239132 at NOS1 98.0 69.9 229975 at BMPR1B 1556606 at 0V2 98.0 69.9 215157 x at PABPC1 1556606 at 0V2 98.0 69.9 208689 s at RPN2 240911 at NOS1 98.0 69.9 204175 at ZNF593 240911 at NOS1 98.0 69.9 213399 x at RPN2 240911 at NOS1 98.0 69.9 218278 at WDR74 240911 at NOS1 98.0 69.9 200619 at SF3B2 240911 at NOS1 98.0 69.9 222572 at PDP1 240911 at NOS1 98.0 69.9 222572 at PDP1 239132 at NOS1 98.0 69.9 225133 at KLF3 240911 at NOS1 98.0 69.9 213491 x at RPN2 240911 at NOS1 98.0 69.9 218823 s at KCTD9 240911 at NOS1 98.0 69.9 203669 s at DGAT1 240911 at NOS1 98.0 69.9 203669 s at DGAT1 239132 at NOS1 98.0 69.9 218656 s at LHFP 240911 at NOS1 98.0 69.9 213391 at DPY19L4 1556606 at 0V2 98.0 69.9 210829 s at SSBP2 240911 at NOS1 98.0 69.9 236926 at TBX1 240911 at NOS1 98.0 69.9 236926 at TBX1 239132 at NOS1 98.0 69.9 200623 s at CALM3 1556606 at 0V2 98.0 69.9 225406 at TWSG1 240911 at NOS1 98.0 69.9 225406 at TWSG1 239132 at NOS1 98.0 69.9 214003 x at RPS20 1556606 at 0V2 98.0 69.9 214649 s at MTMR2 240911 at NOS1 98.0 69.9 200949 x at RPS20 1556606 at 0V2 98.0 69.9 219201 s at TWSG1 240911 at NOS1 98.0 69.9 219201 s at TWSG1 239132 at NOS1 98.0 69.9 1554155 at MCPH1 240911 at NOS1 98.0 69.9 1554155 at MCPH1 231916 at NOS1 98.0 69.9 1554155 at MCPH1 239132 at NOS1 98.0 69.9 222714 s at LACTB2 240911 at NOS1 98.0 69.9 203211 s at MTMR2 240911 at NOS1 98.0 69.9 203211 s at MTMR2 239132 at NOS1 98.0 69.9 208883 at UBR5 240911 at NOS1 98.0 69.9 208883 at UBR5 239132 at NOS1 98.0 69.9 219657 s at KLF3 240911 at NOS1 98.0 69.9 216241 s at TCEA1 240911 at NOS1 98.0 69.2 226814 at ADAMTS9 240911 at NOS1 98.0 69.2 208732 at RAB2A 240911 at NOS1 98.0 69.2 218961 s at PNKP 240911 at NOS1 98.0 69.2 229377 at GRTP1 240911 at NOS1 98.0 69.2 229377 at GRTP1 231916 at NOS1 98.0 69.2 229377 at GRTP1 239132 at NOS1 98.0 69.2 221807 s at TRABD 240911 at NOS1 98.0 69.2 208734 x at RAB2A 240911 at NOS1 98.0 69.2 200617 at MLEC 240911 at NOS1 98.0 69.2 200617 at MLEC 239132 at NOS1 98.0 69.2 1554697 at ADAMTS9 240911 at NOS1 98.0 69.2 208731 at RAB2A 240911 at NOS1 98.0 69.2 202824 s at TCEB1 240911 at NOS1 98.0 69.2 202824 s at TCEB1 239132 at NOS1 98.0 69.2 1555037 a at IDH1 240911 at NOS1 98.0 69.2 201193 at IDH1 240911 at NOS1 98.0 69.2 204068 at STK3 240911 at NOS1 98.0 69.2 204068 at STK3 231916 at NOS1 98.0 69.2 204068 at STK3 239132 at NOS1 98.0 69.2 201783 s at RELA 240911 at NOS1 98.0 69.2 212098 at MGAT5 240911 at NOS1 98.0 69.2 205407 at RECK 240911 at NOS1 98.0 69.2

37 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 205407 at RECK 239132 at NOS1 98.0 69.2 225360 at TRABD 240911 at NOS1 98.0 69.2 221039 s at ASAP1 230076 at PITPNM3 98.0 68.5 224791 at ASAP1 230076 at PITPNM3 98.0 68.5 225676 s at DCAF13 1556606 at 0V2 98.0 68.5 217736 s at EIF2AK1 240911 at NOS1 98.0 68.5 218135 at ERGIC2 240911 at NOS1 98.0 68.5 218135 at ERGIC2 239132 at NOS1 98.0 68.5 208713 at HNRNPUL1 240911 at NOS1 98.0 68.5 208713 at HNRNPUL1 239132 at NOS1 98.0 68.5 231784 s at DCAF13 1556606 at 0V2 98.0 68.5 219072 at BCL7C 240911 at NOS1 98.0 68.5 211126 s at CSRP2 230498 at MCHR1 98.0 68.5 200062 s at RPL30 1556606 at 0V2 98.0 68.5 201745 at TWF1 240911 at NOS1 98.0 68.5 209899 s at PUF60 240911 at NOS1 98.0 68.5 222206 s at NCLN 239132 at NOS1 98.0 68.5 213554 s at CDV3 240911 at NOS1 98.0 68.5 219520 s at WWC3 240911 at NOS1 98.0 68.5 202728 s at LTBP1 240911 at NOS1 98.0 68.5 209218 at SQLE 240911 at NOS1 98.0 68.5 209218 at SQLE 231916 at NOS1 98.0 68.5 209218 at SQLE 239132 at NOS1 98.0 68.5 212724 at RND3 240911 at NOS1 98.0 68.5 207030 s at CSRP2 230498 at MCHR1 98.0 68.5 209418 s at THOC5 240911 at NOS1 98.0 68.5 209418 s at THOC5 239132 at NOS1 98.0 68.5 205990 s at WNT5A 240911 at NOS1 98.0 68.5 209675 s at HNRNPUL1 240911 at NOS1 98.0 68.5 1557331 at POLR1B 1556606 at 0V2 98.0 68.5 207011 s at PTK7 240911 at NOS1 98.0 68.5 214626 s at GA0B 239132 at NOS1 98.0 68.5 202431 s at MYC 240911 at NOS1 98.0 68.5 91952 at DCAF15 240911 at NOS1 98.0 68.5 221767 x at HDLBP 240911 at NOS1 98.0 68.5 211934 x at GA0B 240911 at NOS1 98.0 68.5 202729 s at LTBP1 239132 at NOS1 98.0 68.5 232149 s at NSMAF 240911 at NOS1 98.0 67.8 232149 s at NSMAF 231916 at NOS1 98.0 67.8 232149 s at NSMAF 239132 at NOS1 98.0 67.8 203269 at NSMAF 240911 at NOS1 98.0 67.8 203269 at NSMAF 239132 at NOS1 98.0 67.8 209517 s at ASH2L 240911 at NOS1 98.0 67.8 209517 s at ASH2L 239132 at NOS1 98.0 67.8 219774 at CCDC93 240911 at NOS1 98.0 67.8 219774 at CCDC93 231916 at NOS1 98.0 67.8 219774 at CCDC93 239132 at NOS1 98.0 67.8 214431 at GMPS 240911 at NOS1 98.0 67.8 1558775 s at NSMAF 240911 at NOS1 98.0 67.8 1558775 s at NSMAF 239132 at NOS1 98.0 67.8 208658 at PDIA4 1560974 s at NOS1 98.0 67.8 208658 at PDIA4 240911 at NOS1 98.0 67.8 208658 at PDIA4 231916 at NOS1 98.0 67.8 208658 at PDIA4 239132 at NOS1 98.0 67.8 200717 x at RPL7 240911 at NOS1 98.0 67.8 200717 x at RPL7 239132 at NOS1 98.0 67.8 210811 s at DDX49 240911 at NOS1 98.0 67.8 232148 at NSMAF 240911 at NOS1 98.0 67.8 232148 at NSMAF 239132 at NOS1 98.0 67.8 217092 x at RPL7 240911 at NOS1 98.0 67.8 217092 x at RPL7 239132 at NOS1 98.0 67.8 222417 s at SNX5 240911 at NOS1 98.0 67.1 208882 s at UBR5 230076 at PITPNM3 98.0 67.1 229980 s at SNX5 240911 at NOS1 98.0 67.1 229980 s at SNX5 239132 at NOS1 98.0 67.1 201271 s at RALY 240911 at NOS1 98.0 67.1 217792 at SNX5 240911 at NOS1 98.0 67.1 217792 at SNX5 239132 at NOS1 98.0 67.1

38 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 219060 at WDYHV1 240911 at NOS1 98.0 67.1 219060 at WDYHV1 239132 at NOS1 98.0 67.1 227328 at CAMTA1 240911 at NOS1 98.0 67.1 205770 at GSR 240911 at NOS1 98.0 67.1 217784 at YKT6 240911 at NOS1 98.0 67.1 219231 at TGS1 230498 at MCHR1 98.0 66.4 229975 at BMPR1B 240911 at NOS1 98.0 66.4 229975 at BMPR1B 239132 at NOS1 98.0 66.4 201985 at KIAA0196 240911 at NOS1 98.0 66.4 201985 at KIAA0196 231916 at NOS1 98.0 66.4 201985 at KIAA0196 239132 at NOS1 98.0 66.4 217792 at SNX5 230076 at PITPNM3 98.0 66.4 202722 s at GFPT1 240911 at NOS1 98.0 66.4 213391 at DPY19L4 240911 at NOS1 98.0 66.4 213391 at DPY19L4 231916 at NOS1 98.0 66.4 213391 at DPY19L4 239132 at NOS1 98.0 66.4 202721 s at GFPT1 240911 at NOS1 98.0 66.4 202595 s at LEPROTL1 240911 at NOS1 98.0 66.4 202595 s at LEPROTL1 239132 at NOS1 98.0 66.4 221923 s at NPM1 240911 at NOS1 98.0 66.4 221923 s at NPM1 239132 at NOS1 98.0 66.4 226886 at GFPT1 240911 at NOS1 98.0 66.4 226886 at GFPT1 239132 at NOS1 98.0 66.4 213532 at ADAM17 231916 at NOS1 98.0 65.7 213532 at ADAM17 239132 at NOS1 98.0 65.7 201433 s at PTDSS1 240911 at NOS1 98.0 65.7 235205 at OXR1 240911 at NOS1 98.0 65.7 235205 at OXR1 239132 at NOS1 98.0 65.7 201183 s at CHD4 240911 at NOS1 98.0 65.7 209282 at PRKD2 240911 at NOS1 98.0 65.7 202505 at SNRPB2 240911 at NOS1 98.0 65.7 202505 at SNRPB2 231916 at NOS1 98.0 65.7 202505 at SNRPB2 239132 at NOS1 98.0 65.7 225303 at KIRREL 240911 at NOS1 98.0 65.7 202946 s at BTBD3 240911 at NOS1 98.0 65.7 202946 s at BTBD3 239132 at NOS1 98.0 65.7 225676 s at DCAF13 240911 at NOS1 98.0 65.0 225676 s at DCAF13 239132 at NOS1 98.0 65.0 204849 at TCFL5 240911 at NOS1 98.0 65.0 231784 s at DCAF13 240911 at NOS1 98.0 65.0 231784 s at DCAF13 239132 at NOS1 98.0 65.0 212248 at MTDH 240911 at NOS1 98.0 65.0 212248 at MTDH 239132 at NOS1 98.0 65.0 210950 s at FDFT1 240911 at NOS1 98.0 65.0 210950 s at FDFT1 239132 at NOS1 98.0 65.0 218482 at ENY2 240911 at NOS1 98.0 65.0 218482 at ENY2 239132 at NOS1 98.0 65.0 223165 s at IP6K2 240911 at NOS1 98.0 65.0 219798 s at MEPCE 240911 at NOS1 98.0 65.0 201281 at ADRM1 240911 at NOS1 98.0 65.0 1559822 s at MTDH 240911 at NOS1 98.0 65.0 202670 at MAP2K1 240911 at NOS1 98.0 64.3 202670 at MAP2K1 239132 at NOS1 98.0 64.3 203228 at PAFAH1B3 240911 at NOS1 98.0 64.3 203228 at PAFAH1B3 239132 at NOS1 98.0 64.3 208837 at TMED3 240911 at NOS1 98.0 64.3 203616 at POLB 240911 at NOS1 98.0 64.3 203616 at POLB 231916 at NOS1 98.0 64.3 203616 at POLB 239132 at NOS1 98.0 64.3 203207 s at MTFR1 240911 at NOS1 98.0 64.3 203207 s at MTFR1 239132 at NOS1 98.0 64.3 212166 at XPO7 240911 at NOS1 98.0 64.3 212166 at XPO7 239132 at NOS1 98.0 64.3 215983 s at UBXN8 240911 at NOS1 98.0 64.3 215983 s at UBXN8 239132 at NOS1 98.0 64.3 200608 s at RAD21 240911 at NOS1 98.0 64.3 200608 s at RAD21 231916 at NOS1 98.0 64.3 200608 s at RAD21 239132 at NOS1 98.0 64.3

39 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 202447 at DECR1 240911 at NOS1 98.0 64.3 202447 at DECR1 239132 at NOS1 98.0 64.3 200617 at MLEC 230076 at PITPNM3 98.0 63.6 220967 s at ZNF696 230076 at PITPNM3 98.0 63.6 235311 at FKBP14 240911 at NOS1 98.0 63.6 235311 at FKBP14 239132 at NOS1 98.0 63.6 209406 at BAG2 240911 at NOS1 98.0 62.9 200755 s at CALU 240911 at NOS1 98.0 62.9 200700 s at KDELR2 240911 at NOS1 98.0 62.9 200756 x at CALU 240911 at NOS1 98.0 62.9 208700 s at TKT 240911 at NOS1 98.0 62.9 214845 s at CALU 240911 at NOS1 98.0 62.9 202189 x at PTBP1 240911 at NOS1 98.0 62.2 212015 x at PTBP1 240911 at NOS1 98.0 62.2 216306 x at PTBP1 240911 at NOS1 98.0 62.2 213532 at ADAM17 230076 at PITPNM3 98.0 62.2 211270 x at PTBP1 240911 at NOS1 98.0 62.2 211271 x at PTBP1 240911 at NOS1 98.0 62.2 226421 at AMMECR1 1560974 s at NOS1 98.0 62.2 226421 at AMMECR1 240911 at NOS1 98.0 62.2 226421 at AMMECR1 231916 at NOS1 98.0 62.2 226421 at AMMECR1 239132 at NOS1 98.0 62.2 225676 s at DCAF13 230076 at PITPNM3 98.0 62.2 208842 s at GORASP2 240911 at NOS1 98.0 62.2 208842 s at GORASP2 230076 at PITPNM3 98.0 62.2 208842 s at GORASP2 239132 at NOS1 98.0 62.2 219231 at TGS1 240911 at NOS1 98.0 62.2 219231 at TGS1 231916 at NOS1 98.0 62.2 219231 at TGS1 239132 at NOS1 98.0 62.2 227515 at STAMBP 240911 at NOS1 98.0 62.2 207812 s at GORASP2 240911 at NOS1 98.0 62.2 207812 s at GORASP2 239132 at NOS1 98.0 62.2 215157 x at PABPC1 240911 at NOS1 98.0 62.2 215157 x at PABPC1 230076 at PITPNM3 98.0 62.2 215157 x at PABPC1 239132 at NOS1 98.0 62.2 210296 s at PEX2 240911 at NOS1 98.0 62.2 210296 s at PEX2 231916 at NOS1 98.0 62.2 210296 s at PEX2 239132 at NOS1 98.0 62.2 224206 x at MYNN 240911 at NOS1 98.0 62.2 224206 x at MYNN 231916 at NOS1 98.0 62.2 224206 x at MYNN 239132 at NOS1 98.0 62.2 203737 s at PPRC1 240911 at NOS1 98.0 62.2 203737 s at PPRC1 231916 at NOS1 98.0 62.2 203737 s at PPRC1 239132 at NOS1 98.0 62.2 217946 s at SAE1 240911 at NOS1 98.0 62.2 217946 s at SAE1 230076 at PITPNM3 98.0 62.2 217946 s at SAE1 239132 at NOS1 98.0 62.2 209158 s at CYTH2 240911 at NOS1 98.0 62.2 202758 s at RFXANK 240911 at NOS1 98.0 62.2 222551 s at C8orf33 240911 at NOS1 98.0 62.2 202657 s at SERTAD2 240911 at NOS1 98.0 62.2 208713 at HNRNPUL1 230076 at PITPNM3 98.0 62.2 231784 s at DCAF13 230076 at PITPNM3 98.0 62.2 212885 at MPHOSPH10 240911 at NOS1 98.0 62.2 212885 at MPHOSPH10 239132 at NOS1 98.0 62.2 200970 s at SERP1 240911 at NOS1 98.0 62.2 201252 at PSMC4 240911 at NOS1 98.0 62.2 223216 x at ZNF395 240911 at NOS1 98.0 62.2 223216 x at ZNF395 230076 at PITPNM3 98.0 62.2 223216 x at ZNF395 231916 at NOS1 98.0 62.2 223216 x at ZNF395 239132 at NOS1 98.0 62.2 204976 s at AMMECR1 240911 at NOS1 98.0 62.2 213170 at GPX7 239132 at NOS1 98.0 62.2 200062 s at RPL30 240911 at NOS1 98.0 62.2 200062 s at RPL30 230076 at PITPNM3 98.0 62.2 200062 s at RPL30 239132 at NOS1 98.0 62.2 218159 at DDRGK1 240911 at NOS1 98.0 62.2 208113 x at PABPC3 240911 at NOS1 98.0 62.2

40 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 208113 x at PABPC3 230076 at PITPNM3 98.0 62.2 208113 x at PABPC3 239132 at NOS1 98.0 62.2 208639 x at PDIA6 240911 at NOS1 98.0 62.2 208639 x at PDIA6 239132 at NOS1 98.0 62.2 202656 s at SERTAD2 240911 at NOS1 98.0 62.2 200936 at RPL8 240911 at NOS1 98.0 62.2 200936 at RPL8 239132 at NOS1 98.0 62.2 227684 at S1PR2 240911 at NOS1 98.0 62.2 213564 x at LDHB 240911 at NOS1 98.0 62.2 213564 x at LDHB 230076 at PITPNM3 98.0 62.2 213564 x at LDHB 239132 at NOS1 98.0 62.2 216640 s at PDIA6 240911 at NOS1 98.0 62.2 218388 at PGLS 240911 at NOS1 98.0 62.2 218387 s at PGLS 240911 at NOS1 98.0 62.2 220890 s at DDX47 240911 at NOS1 98.0 62.2 220890 s at DDX47 239132 at NOS1 98.0 62.2 242887 at KCMF1 240911 at NOS1 98.0 62.2 242887 at KCMF1 239132 at NOS1 98.0 62.2 218059 at ZNF706 240911 at NOS1 98.0 62.2 218059 at ZNF706 231916 at NOS1 98.0 62.2 218059 at ZNF706 239132 at NOS1 98.0 62.2 65588 at LOC388796 240911 at NOS1 98.0 62.2 201652 at COPS5 239132 at NOS1 98.0 62.2 222400 s at ADI1 240911 at NOS1 98.0 62.2 201030 x at LDHB 240911 at NOS1 98.0 62.2 201030 x at LDHB 230076 at PITPNM3 98.0 62.2 201030 x at LDHB 239132 at NOS1 98.0 62.2 212016 s at PTBP1 240911 at NOS1 98.0 62.2 208843 s at GORASP2 240911 at NOS1 98.0 62.2 208843 s at GORASP2 239132 at NOS1 98.0 62.2 226949 at GOLGA3 240911 at NOS1 98.0 62.2 221734 at PRRC1 240911 at NOS1 98.0 62.2 219312 s at ZBTB10 240911 at NOS1 98.0 62.2 219312 s at ZBTB10 239132 at NOS1 98.0 62.2 218465 at TMEM33 240911 at NOS1 98.0 62.2 203261 at DCTN6 240911 at NOS1 98.0 62.2 203261 at DCTN6 239132 at NOS1 98.0 62.2 200990 at TRIM28 240911 at NOS1 98.0 62.2 202710 at BET1 240911 at NOS1 98.0 62.2 202710 at BET1 239132 at NOS1 98.0 62.2 209218 at SQLE 230076 at PITPNM3 98.0 62.2 225857 s at LOC388796 240911 at NOS1 98.0 62.2 209817 at PPP3CB 230076 at PITPNM3 98.0 62.2 222694 at MGC2752 240911 at NOS1 98.0 62.2 221770 at RPE 240911 at NOS1 98.0 62.2 200623 s at CALM3 240911 at NOS1 98.0 62.2 200623 s at CALM3 239132 at NOS1 98.0 62.2 221123 x at ZNF395 240911 at NOS1 98.0 62.2 221123 x at ZNF395 239132 at NOS1 98.0 62.2 209808 x at ING1 240911 at NOS1 98.0 62.2 214003 x at RPS20 240911 at NOS1 98.0 62.2 214003 x at RPS20 239132 at NOS1 98.0 62.2 212484 at FAM89B 240911 at NOS1 98.0 62.2 200949 x at RPS20 240911 at NOS1 98.0 62.2 200949 x at RPS20 239132 at NOS1 98.0 62.2 200640 at YWHAZ 240911 at NOS1 98.0 62.2 200640 at YWHAZ 239132 at NOS1 98.0 62.2 221781 s at D0JC10 240911 at NOS1 98.0 62.2 222657 s at UBE2W 240911 at NOS1 98.0 62.2 222657 s at UBE2W 231916 at NOS1 98.0 62.2 222657 s at UBE2W 239132 at NOS1 98.0 62.2 1556429 a at WDR67 240911 at NOS1 98.0 62.2 1556429 a at WDR67 239132 at NOS1 98.0 62.2 202635 s at POLR2K 240911 at NOS1 98.0 62.2 202635 s at POLR2K 239132 at NOS1 98.0 62.2 200922 at KDELR1 240911 at NOS1 98.0 62.2 218932 at ZNHIT6 240911 at NOS1 98.0 62.2 218932 at ZNHIT6 239132 at NOS1 98.0 62.2

41 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 210137 s at DCTD 240911 at NOS1 98.0 62.2 207668 x at PDIA6 240911 at NOS1 98.0 62.2 207668 x at PDIA6 239132 at NOS1 98.0 62.2 219126 at PHF10 240911 at NOS1 98.0 62.2 201571 s at DCTD 240911 at NOS1 98.0 62.2 222654 at IMPAD1 240911 at NOS1 98.0 62.2 222654 at IMPAD1 230076 at PITPNM3 98.0 62.2 222654 at IMPAD1 239132 at NOS1 98.0 62.2 221786 at C6orf120 240911 at NOS1 98.0 62.2 220147 s at FAM60A 240911 at NOS1 98.0 62.2 218926 at MYNN 240911 at NOS1 98.0 62.2 218926 at MYNN 231916 at NOS1 98.0 62.2 218926 at MYNN 239132 at NOS1 98.0 62.2 232012 at CAPN1 240911 at NOS1 98.0 62.2 232012 at CAPN1 239132 at NOS1 98.0 62.2 200639 s at YWHAZ 240911 at NOS1 98.0 62.2 200639 s at YWHAZ 231916 at NOS1 98.0 62.2 200639 s at YWHAZ 239132 at NOS1 98.0 62.2 201754 at COX6C 240911 at NOS1 98.0 62.2 221586 s at E2F5 230076 at PITPNM3 98.0 62.2 200969 at SERP1 240911 at NOS1 98.0 62.2 1555618 s at SAE1 240911 at NOS1 98.0 62.2 201592 at EIF3H 240911 at NOS1 98.0 62.2 201592 at EIF3H 230076 at PITPNM3 98.0 62.2 201592 at EIF3H 239132 at NOS1 98.0 62.2 204392 at CAMK1 240911 at NOS1 98.0 62.2 218904 s at C9orf40 240911 at NOS1 98.0 62.2 209953 s at CDC37 240911 at NOS1 98.0 62.2 207266 x at RBMS1 240911 at NOS1 98.0 62.2 200608 s at RAD21 230076 at PITPNM3 98.0 62.2 212481 s at TPM4 240911 at NOS1 98.0 62.2 225267 at KP04 240911 at NOS1 98.0 62.2 226886 at GFPT1 230076 at PITPNM3 98.0 62.2 212194 s at TM9SF4 240911 at NOS1 98.0 62.2 214512 s at SUB1 240911 at NOS1 98.0 62.2 202033 s at RB1CC1 239132 at NOS1 98.0 62.2 219231 at TGS1 230076 at PITPNM3 98.0 60.1 203184 at FBN2 244409 at CCDC154 98.0 ··· 225288 at COL27A1 204094 s at TSC22D2 98.0 ··· 225288 at COL27A1 222912 at ARRB1 98.0 ··· 225288 at COL27A1 233632 s at XRN1 98.0 ··· 225288 at COL27A1 225814 at XRN1 98.0 ··· 225288 at COL27A1 244409 at CCDC154 98.0 ··· 225288 at COL27A1 240911 at NOS1 98.0 ··· 225288 at COL27A1 221605 s at PIPOX 98.0 ··· 225288 at COL27A1 231916 at NOS1 98.0 ··· 225288 at COL27A1 239132 at NOS1 98.0 ··· 219570 at KIF16B 1553394 a at TFAP2B 98.0 ··· 219570 at KIF16B 244409 at CCDC154 98.0 ··· 212458 at SPRED2 223741 s at TTYH2 98.0 ··· 212458 at SPRED2 225814 at XRN1 98.0 ··· 212458 at SPRED2 244409 at CCDC154 98.0 ··· 221039 s at ASAP1 233632 s at XRN1 98.0 ··· 221039 s at ASAP1 225814 at XRN1 98.0 ··· 221039 s at ASAP1 244409 at CCDC154 98.0 ··· 201121 s at PGRMC1 233632 s at XRN1 98.0 ··· 201121 s at PGRMC1 244409 at CCDC154 98.0 ··· 232083 at KIF16B 226443 at FAM122A 98.0 ··· 232083 at KIF16B 244824 at NA 98.0 ··· 232083 at KIF16B 225306 s at SLC25A29 98.0 ··· 232083 at KIF16B 225814 at XRN1 98.0 ··· 232083 at KIF16B 244409 at CCDC154 98.0 ··· 222199 s at BIN3 223974 at MGC11082 98.0 ··· 222199 s at BIN3 244409 at CCDC154 98.0 ··· 203706 s at FZD7 233632 s at XRN1 98.0 ··· 203706 s at FZD7 225814 at XRN1 98.0 ··· 203706 s at FZD7 244409 at CCDC154 98.0 ··· 203355 s at PSD3 225814 at XRN1 98.0 ···

42 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 203355 s at PSD3 244409 at CCDC154 98.0 ··· 203705 s at FZD7 233632 s at XRN1 98.0 ··· 203705 s at FZD7 244409 at CCDC154 98.0 ··· 202189 x at PTBP1 244409 at CCDC154 98.0 ··· 216241 s at TCEA1 244409 at CCDC154 98.0 ··· 218816 at LRRC1 233632 s at XRN1 98.0 ··· 218816 at LRRC1 225814 at XRN1 98.0 ··· 218816 at LRRC1 244409 at CCDC154 98.0 ··· 225293 at COL27A1 225814 at XRN1 98.0 ··· 225293 at COL27A1 244409 at CCDC154 98.0 ··· 225293 at COL27A1 240911 at NOS1 98.0 ··· 225293 at COL27A1 221605 s at PIPOX 98.0 ··· 225293 at COL27A1 239132 at NOS1 98.0 ··· 211737 x at PTN 244409 at CCDC154 98.0 ··· 214721 x at CDC42EP4 233632 s at XRN1 98.0 ··· 214721 x at CDC42EP4 244409 at CCDC154 98.0 ··· 224796 at ASAP1 233632 s at XRN1 98.0 ··· 224796 at ASAP1 225814 at XRN1 98.0 ··· 224796 at ASAP1 244409 at CCDC154 98.0 ··· 223282 at TSHZ1 1554628 at ZNF57 98.0 ··· 223282 at TSHZ1 228170 at OLIG1 98.0 ··· 223282 at TSHZ1 233632 s at XRN1 98.0 ··· 223282 at TSHZ1 244409 at CCDC154 98.0 ··· 223282 at TSHZ1 240911 at NOS1 98.0 ··· 223282 at TSHZ1 230076 at PITPNM3 98.0 ··· 223282 at TSHZ1 1556606 at 0V2 98.0 ··· 223282 at TSHZ1 231916 at NOS1 98.0 ··· 223282 at TSHZ1 239132 at NOS1 98.0 ··· 212015 x at PTBP1 244409 at CCDC154 98.0 ··· 224999 at EGFR 233632 s at XRN1 98.0 ··· 224999 at EGFR 225814 at XRN1 98.0 ··· 224999 at EGFR 244409 at CCDC154 98.0 ··· 224999 at EGFR 214451 at TFAP2B 98.0 ··· 225975 at PCDH18 244409 at CCDC154 98.0 ··· 225975 at PCDH18 240911 at NOS1 98.0 ··· 225975 at PCDH18 214451 at TFAP2B 98.0 ··· 225975 at PCDH18 239132 at NOS1 98.0 ··· 216306 x at PTBP1 244409 at CCDC154 98.0 ··· 218974 at SOBP 233632 s at XRN1 98.0 ··· 218974 at SOBP 244409 at CCDC154 98.0 ··· 222651 s at TRPS1 244409 at CCDC154 98.0 ··· 222651 s at TRPS1 214451 at TFAP2B 98.0 ··· 218613 at PSD3 233632 s at XRN1 98.0 ··· 218613 at PSD3 244409 at CCDC154 98.0 ··· 213532 at ADAM17 244409 at CCDC154 98.0 ··· 1555889 a at CRTAP 225814 at XRN1 98.0 ··· 1555889 a at CRTAP 244409 at CCDC154 98.0 ··· 218502 s at TRPS1 244409 at CCDC154 98.0 ··· 229228 at CREB5 233632 s at XRN1 98.0 ··· 229228 at CREB5 244409 at CCDC154 98.0 ··· 211270 x at PTBP1 244409 at CCDC154 98.0 ··· 238520 at TRERF1 244409 at CCDC154 98.0 ··· 220233 at NA 244409 at CCDC154 98.0 ··· 220233 at NA 240911 at NOS1 98.0 ··· 220233 at NA 239132 at NOS1 98.0 ··· 209465 x at PTN 244409 at CCDC154 98.0 ··· 202680 at GTF2E2 238432 at FLJ35776 98.0 ··· 202680 at GTF2E2 223974 at MGC11082 98.0 ··· 202680 at GTF2E2 244409 at CCDC154 98.0 ··· 241342 at TMEM65 233632 s at XRN1 98.0 ··· 241342 at TMEM65 225814 at XRN1 98.0 ··· 241342 at TMEM65 244409 at CCDC154 98.0 ··· 241342 at TMEM65 214451 at TFAP2B 98.0 ··· 241342 at TMEM65 221605 s at PIPOX 98.0 ··· 241342 at TMEM65 239132 at NOS1 98.0 ··· 235334 at ST6GAL0C3 244409 at CCDC154 98.0 ··· 235334 at ST6GAL0C3 240911 at NOS1 98.0 ··· 220911 s at NYNRIN 225814 at XRN1 98.0 ···

43 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 220911 s at NYNRIN 1553394 a at TFAP2B 98.0 ··· 220911 s at NYNRIN 244409 at CCDC154 98.0 ··· 224791 at ASAP1 233632 s at XRN1 98.0 ··· 224791 at ASAP1 225814 at XRN1 98.0 ··· 224791 at ASAP1 244409 at CCDC154 98.0 ··· 223283 s at TSHZ1 1554628 at ZNF57 98.0 ··· 223283 s at TSHZ1 233632 s at XRN1 98.0 ··· 223283 s at TSHZ1 244409 at CCDC154 98.0 ··· 223283 s at TSHZ1 240911 at NOS1 98.0 ··· 227550 at GFRA1 233632 s at XRN1 98.0 ··· 227550 at GFRA1 225814 at XRN1 98.0 ··· 227550 at GFRA1 244409 at CCDC154 98.0 ··· 227550 at GFRA1 221605 s at PIPOX 98.0 ··· 224790 at ASAP1 233632 s at XRN1 98.0 ··· 224790 at ASAP1 225814 at XRN1 98.0 ··· 224790 at ASAP1 244409 at CCDC154 98.0 ··· 211271 x at PTBP1 244409 at CCDC154 98.0 ··· 225292 at COL27A1 244409 at CCDC154 98.0 ··· 225292 at COL27A1 240911 at NOS1 98.0 ··· 225292 at COL27A1 214451 at TFAP2B 98.0 ··· 225292 at COL27A1 239132 at NOS1 98.0 ··· 227864 s at FAM125A 244409 at CCDC154 98.0 ··· 227864 s at FAM125A 240911 at NOS1 98.0 ··· 228171 s at PLEKHG4 206446 s at NA 98.0 ··· 228171 s at PLEKHG4 244409 at CCDC154 98.0 ··· 228171 s at PLEKHG4 240911 at NOS1 98.0 ··· 228171 s at PLEKHG4 239132 at NOS1 98.0 ··· 221958 s at WLS 233632 s at XRN1 98.0 ··· 221958 s at WLS 225814 at XRN1 98.0 ··· 221958 s at WLS 244409 at CCDC154 98.0 ··· 221958 s at WLS 240911 at NOS1 98.0 ··· 213478 at KAZN 233632 s at XRN1 98.0 ··· 213478 at KAZN 244409 at CCDC154 98.0 ··· 213478 at KAZN 240911 at NOS1 98.0 ··· 232653 at NA 244409 at CCDC154 98.0 ··· 232653 at NA 240911 at NOS1 98.0 ··· 232653 at NA 214451 at TFAP2B 98.0 ··· 232653 at NA 239132 at NOS1 98.0 ··· 201905 s at CTDSPL 244409 at CCDC154 98.0 ··· 226834 at NA 207076 s at ASS1 98.0 ··· 226834 at NA 244409 at CCDC154 98.0 ··· 226834 at NA 240911 at NOS1 98.0 ··· 226834 at NA 214451 at TFAP2B 98.0 ··· 217788 s at GALNT2 244409 at CCDC154 98.0 ··· 223475 at CRISPLD1 244409 at CCDC154 98.0 ··· 223475 at CRISPLD1 239132 at NOS1 98.0 ··· 244579 at NA 244409 at CCDC154 98.0 ··· 244579 at NA 240911 at NOS1 98.0 ··· 244579 at NA 214451 at TFAP2B 98.0 ··· 244579 at NA 239132 at NOS1 98.0 ··· 226421 at AMMECR1 244409 at CCDC154 98.0 ··· 225702 at C8orf76 233632 s at XRN1 98.0 ··· 225702 at C8orf76 225814 at XRN1 98.0 ··· 225702 at C8orf76 244409 at CCDC154 98.0 ··· 225702 at C8orf76 240911 at NOS1 98.0 ··· 225702 at C8orf76 1556606 at 0V2 98.0 ··· 225702 at C8orf76 221605 s at PIPOX 98.0 ··· 225702 at C8orf76 231916 at NOS1 98.0 ··· 225702 at C8orf76 239132 at NOS1 98.0 ··· 1554464 a at CRTAP 233632 s at XRN1 98.0 ··· 1554464 a at CRTAP 225814 at XRN1 98.0 ··· 1554464 a at CRTAP 244409 at CCDC154 98.0 ··· 239153 at HOTAIR 244409 at CCDC154 98.0 ··· 239153 at HOTAIR 240911 at NOS1 98.0 ··· 239153 at HOTAIR 1556606 at 0V2 98.0 ··· 239153 at HOTAIR 221605 s at PIPOX 98.0 ··· 239153 at HOTAIR 239132 at NOS1 98.0 ··· 218062 x at CDC42EP4 233632 s at XRN1 98.0 ···

44 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 218062 x at CDC42EP4 244409 at CCDC154 98.0 ··· 218959 at HOXC10 244409 at CCDC154 98.0 ··· 226384 at PPAPDC1B 233632 s at XRN1 98.0 ··· 226384 at PPAPDC1B 225814 at XRN1 98.0 ··· 226384 at PPAPDC1B 244409 at CCDC154 98.0 ··· 226384 at PPAPDC1B 240911 at NOS1 98.0 ··· 226384 at PPAPDC1B 1556606 at 0V2 98.0 ··· 226384 at PPAPDC1B 221605 s at PIPOX 98.0 ··· 226384 at PPAPDC1B 239132 at NOS1 98.0 ··· 227616 at BCL9L 244409 at CCDC154 98.0 ··· 227616 at BCL9L 240911 at NOS1 98.0 ··· 221000 s at KAZALD1 229125 at KANK4 98.0 ··· 221000 s at KAZALD1 244409 at CCDC154 98.0 ··· 232149 s at NSMAF 244409 at CCDC154 98.0 ··· 232149 s at NSMAF 221605 s at PIPOX 98.0 ··· 211686 s at MAK16 238432 at FLJ35776 98.0 ··· 211686 s at MAK16 223974 at MGC11082 98.0 ··· 211686 s at MAK16 244409 at CCDC154 98.0 ··· 209466 x at PTN 244409 at CCDC154 98.0 ··· 228904 at HOXB3 244409 at CCDC154 98.0 ··· 226464 at C3orf58 207076 s at ASS1 98.0 ··· 226464 at C3orf58 244409 at CCDC154 98.0 ··· 226464 at C3orf58 240911 at NOS1 98.0 ··· 226464 at C3orf58 214451 at TFAP2B 98.0 ··· 226464 at C3orf58 213436 at CNR1 98.0 ··· 226464 at C3orf58 1556606 at 0V2 98.0 ··· 226464 at C3orf58 239132 at NOS1 98.0 ··· 209883 at GLT25D2 244409 at CCDC154 98.0 ··· 241700 at ZFHX4 244409 at CCDC154 98.0 ··· 225676 s at DCAF13 244409 at CCDC154 98.0 ··· 202907 s at NBN 233632 s at XRN1 98.0 ··· 202907 s at NBN 244409 at CCDC154 98.0 ··· 203269 at NSMAF 225814 at XRN1 98.0 ··· 203269 at NSMAF 244409 at CCDC154 98.0 ··· 224218 s at TRPS1 244409 at CCDC154 98.0 ··· 227243 s at EBF3 244409 at CCDC154 98.0 ··· 227243 s at EBF3 240911 at NOS1 98.0 ··· 227243 s at EBF3 221605 s at PIPOX 98.0 ··· 227243 s at EBF3 239132 at NOS1 98.0 ··· 201984 s at EGFR 244409 at CCDC154 98.0 ··· 221020 s at SLC25A32 244409 at CCDC154 98.0 ··· 225977 at PCDH18 233632 s at XRN1 98.0 ··· 225977 at PCDH18 244409 at CCDC154 98.0 ··· 225977 at PCDH18 240911 at NOS1 98.0 ··· 215138 s at KAZN 244409 at CCDC154 98.0 ··· 215138 s at KAZN 240911 at NOS1 98.0 ··· 221539 at EIF4EBP1 244409 at CCDC154 98.0 ··· 212867 at NCOA2 244409 at CCDC154 98.0 ··· 201787 at FBLN1 244409 at CCDC154 98.0 ··· 200824 at GSTP1 244409 at CCDC154 98.0 ··· 227242 s at EBF3 244409 at CCDC154 98.0 ··· 227242 s at EBF3 240911 at NOS1 98.0 ··· 207424 at MYF5 244409 at CCDC154 98.0 ··· 228950 s at WLS 233632 s at XRN1 98.0 ··· 228950 s at WLS 225814 at XRN1 98.0 ··· 228950 s at WLS 244409 at CCDC154 98.0 ··· 228950 s at WLS 240911 at NOS1 98.0 ··· 223991 s at GALNT2 233632 s at XRN1 98.0 ··· 223991 s at GALNT2 244409 at CCDC154 98.0 ··· 208842 s at GORASP2 244409 at CCDC154 98.0 ··· 222417 s at SNX5 244409 at CCDC154 98.0 ··· 211518 s at BMP4 244409 at CCDC154 98.0 ··· 236270 at NFATC4 244409 at CCDC154 98.0 ··· 208882 s at UBR5 244409 at CCDC154 98.0 ··· 201644 at TSTA3 244409 at CCDC154 98.0 ··· 204442 x at LTBP4 244409 at CCDC154 98.0 ··· 219231 at TGS1 1562659 at LOC400548 98.0 ··· 219231 at TGS1 1560019 at MGC11082 98.0 ···

45 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 219231 at TGS1 244409 at CCDC154 98.0 ··· 202786 at STK39 233632 s at XRN1 98.0 ··· 202786 at STK39 225814 at XRN1 98.0 ··· 202786 at STK39 244409 at CCDC154 98.0 ··· 223125 s at C1orf21 244409 at CCDC154 98.0 ··· 1568955 at SRGAP2P1 206447 at NA 98.0 ··· 1568955 at SRGAP2P1 244409 at CCDC154 98.0 ··· 1568955 at SRGAP2P1 240911 at NOS1 98.0 ··· 1568955 at SRGAP2P1 230076 at PITPNM3 98.0 ··· 1568955 at SRGAP2P1 221605 s at PIPOX 98.0 ··· 1568955 at SRGAP2P1 231916 at NOS1 98.0 ··· 1568955 at SRGAP2P1 239132 at NOS1 98.0 ··· 217787 s at GALNT2 233632 s at XRN1 98.0 ··· 217787 s at GALNT2 244409 at CCDC154 98.0 ··· 223023 at BET1L 233632 s at XRN1 98.0 ··· 223023 at BET1L 225814 at XRN1 98.0 ··· 223023 at BET1L 244409 at CCDC154 98.0 ··· 235355 at CSRNP3 244409 at CCDC154 98.0 ··· 233257 at NA 244409 at CCDC154 98.0 ··· 233257 at NA 240911 at NOS1 98.0 ··· 233257 at NA 1556606 at 0V2 98.0 ··· 233257 at NA 221605 s at PIPOX 98.0 ··· 233257 at NA 239132 at NOS1 98.0 ··· 225510 at OAF 225814 at XRN1 98.0 ··· 225510 at OAF 244409 at CCDC154 98.0 ··· 225510 at OAF 240911 at NOS1 98.0 ··· 201939 at PLK2 244409 at CCDC154 98.0 ··· 226868 at GXYLT1 206446 s at NA 98.0 ··· 226868 at GXYLT1 225814 at XRN1 98.0 ··· 226868 at GXYLT1 244409 at CCDC154 98.0 ··· 226868 at GXYLT1 240911 at NOS1 98.0 ··· 226868 at GXYLT1 1556606 at 0V2 98.0 ··· 226868 at GXYLT1 231916 at NOS1 98.0 ··· 226868 at GXYLT1 239132 at NOS1 98.0 ··· 201398 s at TRAM1 233632 s at XRN1 98.0 ··· 201398 s at TRAM1 225814 at XRN1 98.0 ··· 201398 s at TRAM1 244409 at CCDC154 98.0 ··· 235012 at LRCH1 233632 s at XRN1 98.0 ··· 235012 at LRCH1 225814 at XRN1 98.0 ··· 235012 at LRCH1 244409 at CCDC154 98.0 ··· 204015 s at DUSP4 244409 at CCDC154 98.0 ··· 229980 s at SNX5 244409 at CCDC154 98.0 ··· 204235 s at GULP1 244409 at CCDC154 98.0 ··· 203941 at INTS9 223974 at MGC11082 98.0 ··· 203941 at INTS9 244409 at CCDC154 98.0 ··· 226795 at LRCH1 233632 s at XRN1 98.0 ··· 226795 at LRCH1 225814 at XRN1 98.0 ··· 226795 at LRCH1 244409 at CCDC154 98.0 ··· 229144 at KAZN 244409 at CCDC154 98.0 ··· 229144 at KAZN 240911 at NOS1 98.0 ··· 204036 at LPAR1 233632 s at XRN1 98.0 ··· 204036 at LPAR1 225814 at XRN1 98.0 ··· 204036 at LPAR1 244409 at CCDC154 98.0 ··· 218689 at FANCF 233632 s at XRN1 98.0 ··· 218689 at FANCF 225814 at XRN1 98.0 ··· 218689 at FANCF 244409 at CCDC154 98.0 ··· 221959 at FAM110B 244409 at CCDC154 98.0 ··· 209129 at TRIP6 244409 at CCDC154 98.0 ··· 225439 at NUDCD1 238432 at FLJ35776 98.0 ··· 225439 at NUDCD1 244409 at CCDC154 98.0 ··· 225439 at NUDCD1 240911 at NOS1 98.0 ··· 225439 at NUDCD1 1556606 at 0V2 98.0 ··· 225439 at NUDCD1 221605 s at PIPOX 98.0 ··· 202479 s at TRIB2 233632 s at XRN1 98.0 ··· 202479 s at TRIB2 244409 at CCDC154 98.0 ··· 205848 at GAS2 244409 at CCDC154 98.0 ··· 228837 at TCF4 244409 at CCDC154 98.0 ··· 235509 at C8orf38 244409 at CCDC154 98.0 ···

46 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 235509 at C8orf38 240911 at NOS1 98.0 ··· 235509 at C8orf38 239132 at NOS1 98.0 ··· 243041 s at NA 244409 at CCDC154 98.0 ··· 243041 s at NA 240911 at NOS1 98.0 ··· 243041 s at NA 239132 at NOS1 98.0 ··· 204037 at LPAR1 233632 s at XRN1 98.0 ··· 204037 at LPAR1 225814 at XRN1 98.0 ··· 204037 at LPAR1 244409 at CCDC154 98.0 ··· 202905 x at NBN 244409 at CCDC154 98.0 ··· 201368 at ZFP36L2 233632 s at XRN1 98.0 ··· 201368 at ZFP36L2 225814 at XRN1 98.0 ··· 201368 at ZFP36L2 244409 at CCDC154 98.0 ··· 1568598 at KAZALD1 244409 at CCDC154 98.0 ··· 227860 at CPXM1 244409 at CCDC154 98.0 ··· 227860 at CPXM1 240911 at NOS1 98.0 ··· 36936 at TSTA3 244409 at CCDC154 98.0 ··· 208025 s at HMGA2 244409 at CCDC154 98.0 ··· 224710 at RAB34 244409 at CCDC154 98.0 ··· 224710 at RAB34 240911 at NOS1 98.0 ··· 229009 at SIX5 244409 at CCDC154 98.0 ··· 229569 at NA 244409 at CCDC154 98.0 ··· 229569 at NA 240911 at NOS1 98.0 ··· 202423 at KAT6A 244409 at CCDC154 98.0 ··· 202423 at KAT6A 240911 at NOS1 98.0 ··· 202423 at KAT6A 1556606 at 0V2 98.0 ··· 202423 at KAT6A 231916 at NOS1 98.0 ··· 202423 at KAT6A 239132 at NOS1 98.0 ··· 212313 at CHMP7 244409 at CCDC154 98.0 ··· 209441 at RHOBTB2 244409 at CCDC154 98.0 ··· 1556638 at PAX7 244409 at CCDC154 98.0 ··· 1556638 at PAX7 221605 s at PIPOX 98.0 ··· 212360 at AMPD2 244409 at CCDC154 98.0 ··· 219894 at MAGEL2 244409 at CCDC154 98.0 ··· 212445 s at NEDD4L 225306 s at SLC25A29 98.0 ··· 212445 s at NEDD4L 233632 s at XRN1 98.0 ··· 212445 s at NEDD4L 225814 at XRN1 98.0 ··· 212445 s at NEDD4L 244409 at CCDC154 98.0 ··· 218665 at FZD4 233632 s at XRN1 98.0 ··· 218665 at FZD4 225814 at XRN1 98.0 ··· 218665 at FZD4 244409 at CCDC154 98.0 ··· 226814 at ADAMTS9 233632 s at XRN1 98.0 ··· 226814 at ADAMTS9 225814 at XRN1 98.0 ··· 226814 at ADAMTS9 244409 at CCDC154 98.0 ··· 204087 s at SLC5A6 244409 at CCDC154 98.0 ··· 208884 s at UBR5 244409 at CCDC154 98.0 ··· 213752 at KAZN 229024 at NA 98.0 ··· 213752 at KAZN 244409 at CCDC154 98.0 ··· 213752 at KAZN 240911 at NOS1 98.0 ··· 225802 at TOP1MT 238432 at FLJ35776 98.0 ··· 225802 at TOP1MT 244409 at CCDC154 98.0 ··· 225802 at TOP1MT 240911 at NOS1 98.0 ··· 225802 at TOP1MT 230076 at PITPNM3 98.0 ··· 225802 at TOP1MT 221605 s at PIPOX 98.0 ··· 225802 at TOP1MT 239132 at NOS1 98.0 ··· 210023 s at PCGF1 244409 at CCDC154 98.0 ··· 225168 at FRMD4A 225814 at XRN1 98.0 ··· 225168 at FRMD4A 244409 at CCDC154 98.0 ··· 208675 s at DDOST 244409 at CCDC154 98.0 ··· 1552658 a at 0V3 244409 at CCDC154 98.0 ··· 222713 s at FANCF 233632 s at XRN1 98.0 ··· 222713 s at FANCF 244409 at CCDC154 98.0 ··· 223110 at KIAA1429 244409 at CCDC154 98.0 ··· 223110 at KIAA1429 240911 at NOS1 98.0 ··· 223110 at KIAA1429 1556606 at 0V2 98.0 ··· 223110 at KIAA1429 221605 s at PIPOX 98.0 ··· 223110 at KIAA1429 231916 at NOS1 98.0 ··· 223110 at KIAA1429 239132 at NOS1 98.0 ··· 206302 s at NA 244409 at CCDC154 98.0 ···

47 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 206302 s at NA 240911 at NOS1 98.0 ··· 217736 s at EIF2AK1 244409 at CCDC154 98.0 ··· 217999 s at PHLDA1 244409 at CCDC154 98.0 ··· 221582 at HIST3H2A 244409 at CCDC154 98.0 ··· 219837 s at CYTL1 244409 at CCDC154 98.0 ··· 227506 at SLC16A9 244409 at CCDC154 98.0 ··· 227506 at SLC16A9 240911 at NOS1 98.0 ··· 227506 at SLC16A9 230076 at PITPNM3 98.0 ··· 227515 at STAMBP 244409 at CCDC154 98.0 ··· 209535 s at NA 244409 at CCDC154 98.0 ··· 209535 s at NA 240911 at NOS1 98.0 ··· 209535 s at NA 230076 at PITPNM3 98.0 ··· 209535 s at NA 231916 at NOS1 98.0 ··· 209535 s at NA 239132 at NOS1 98.0 ··· 1555630 a at RAB34 244409 at CCDC154 98.0 ··· 1555630 a at RAB34 240911 at NOS1 98.0 ··· 202925 s at PLAGL2 244409 at CCDC154 98.0 ··· 203426 s at IGFBP5 244409 at CCDC154 98.0 ··· 206303 s at NUDT4 244409 at CCDC154 98.0 ··· 226547 at KAT6A 206446 s at NA 98.0 ··· 226547 at KAT6A 244409 at CCDC154 98.0 ··· 226547 at KAT6A 240911 at NOS1 98.0 ··· 226547 at KAT6A 230076 at PITPNM3 98.0 ··· 226547 at KAT6A 1556606 at 0V2 98.0 ··· 226547 at KAT6A 239132 at NOS1 98.0 ··· 201271 s at RALY 244409 at CCDC154 98.0 ··· 222853 at FLRT3 244409 at CCDC154 98.0 ··· 219511 s at SNCAIP 244409 at CCDC154 98.0 ··· 213342 at YAP1 233632 s at XRN1 98.0 ··· 213342 at YAP1 225814 at XRN1 98.0 ··· 213342 at YAP1 244409 at CCDC154 98.0 ··· 223568 s at PPAPDC1B 244409 at CCDC154 98.0 ··· 223568 s at PPAPDC1B 240911 at NOS1 98.0 ··· 223568 s at PPAPDC1B 1556606 at 0V2 98.0 ··· 223568 s at PPAPDC1B 239132 at NOS1 98.0 ··· 204404 at SLC12A2 244409 at CCDC154 98.0 ··· 219884 at LHX6 244409 at CCDC154 98.0 ··· 208916 at SLC1A5 244409 at CCDC154 98.0 ··· 219675 s at UXS1 244409 at CCDC154 98.0 ··· 226278 at SVIP 225814 at XRN1 98.0 ··· 226278 at SVIP 244409 at CCDC154 98.0 ··· 226278 at SVIP 240911 at NOS1 98.0 ··· 233422 at NA 233632 s at XRN1 98.0 ··· 233422 at NA 244409 at CCDC154 98.0 ··· 233422 at NA 240911 at NOS1 98.0 ··· 233422 at NA 1556606 at 0V2 98.0 ··· 233422 at NA 221605 s at PIPOX 98.0 ··· 233422 at NA 239132 at NOS1 98.0 ··· 225167 at FRMD4A 244409 at CCDC154 98.0 ··· 215913 s at GULP1 233632 s at XRN1 98.0 ··· 215913 s at GULP1 244409 at CCDC154 98.0 ··· 201618 x at GPAA1 240744 at CPA5 98.0 ··· 201618 x at GPAA1 244409 at CCDC154 98.0 ··· 229975 at BMPR1B 225814 at XRN1 98.0 ··· 229975 at BMPR1B 244409 at CCDC154 98.0 ··· 205522 at NA 244409 at CCDC154 98.0 ··· 205522 at NA 240911 at NOS1 98.0 ··· 205522 at NA 239132 at NOS1 98.0 ··· 207812 s at GORASP2 244409 at CCDC154 98.0 ··· 205107 s at EF04 225814 at XRN1 98.0 ··· 205107 s at EF04 244409 at CCDC154 98.0 ··· 203488 at LPHN1 244409 at CCDC154 98.0 ··· 227992 s at LINC00085 244409 at CCDC154 98.0 ··· 227992 s at LINC00085 240911 at NOS1 98.0 ··· 227992 s at LINC00085 239132 at NOS1 98.0 ··· 207118 s at NA 225306 s at SLC25A29 98.0 ··· 207118 s at NA 244409 at CCDC154 98.0 ··· 207118 s at NA 240911 at NOS1 98.0 ···

48 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 201120 s at PGRMC1 233632 s at XRN1 98.0 ··· 201120 s at PGRMC1 244409 at CCDC154 98.0 ··· 227836 at UTP23 233632 s at XRN1 98.0 ··· 227836 at UTP23 206446 s at NA 98.0 ··· 227836 at UTP23 244409 at CCDC154 98.0 ··· 227836 at UTP23 240911 at NOS1 98.0 ··· 227836 at UTP23 1556606 at 0V2 98.0 ··· 227836 at UTP23 221605 s at PIPOX 98.0 ··· 227836 at UTP23 231916 at NOS1 98.0 ··· 227836 at UTP23 239132 at NOS1 98.0 ··· 201995 at EXT1 233632 s at XRN1 98.0 ··· 201995 at EXT1 244409 at CCDC154 98.0 ··· 215157 x at PABPC1 244409 at CCDC154 98.0 ··· 225583 at UXS1 244409 at CCDC154 98.0 ··· 210296 s at PEX2 244409 at CCDC154 98.0 ··· 219250 s at FLRT3 233632 s at XRN1 98.0 ··· 219250 s at FLRT3 244409 at CCDC154 98.0 ··· 219548 at ZNF16 244409 at CCDC154 98.0 ··· 201206 s at RRBP1 233632 s at XRN1 98.0 ··· 201206 s at RRBP1 244409 at CCDC154 98.0 ··· 1568957 x at SRGAP2P1 244409 at CCDC154 98.0 ··· 1568957 x at SRGAP2P1 240911 at NOS1 98.0 ··· 1568957 x at SRGAP2P1 221605 s at PIPOX 98.0 ··· 1568957 x at SRGAP2P1 231916 at NOS1 98.0 ··· 1568957 x at SRGAP2P1 239132 at NOS1 98.0 ··· 218839 at HEY1 244409 at CCDC154 98.0 ··· 218905 at INTS8 233632 s at XRN1 98.0 ··· 218905 at INTS8 244409 at CCDC154 98.0 ··· 217998 at PHLDA1 244409 at CCDC154 98.0 ··· 208674 x at DDOST 244409 at CCDC154 98.0 ··· 235457 at MAML2 233632 s at XRN1 98.0 ··· 235457 at MAML2 225814 at XRN1 98.0 ··· 235457 at MAML2 244409 at CCDC154 98.0 ··· 235457 at MAML2 240911 at NOS1 98.0 ··· 204823 at 0V3 244409 at CCDC154 98.0 ··· 206767 at RBMS3 233632 s at XRN1 98.0 ··· 206767 at RBMS3 244409 at CCDC154 98.0 ··· 225547 at SNHG6 244409 at CCDC154 98.0 ··· 225547 at SNHG6 240911 at NOS1 98.0 ··· 225547 at SNHG6 1556606 at 0V2 98.0 ··· 226034 at DUSP4 244409 at CCDC154 98.0 ··· 226034 at DUSP4 221605 s at PIPOX 98.0 ··· 203417 at MFAP2 244409 at CCDC154 98.0 ··· 216705 s at ADA 244409 at CCDC154 98.0 ··· 209517 s at ASH2L 244409 at CCDC154 98.0 ··· 1558290 a at PVT1 244409 at CCDC154 98.0 ··· 225010 at CCDC6 244409 at CCDC154 98.0 ··· 204237 at GULP1 233632 s at XRN1 98.0 ··· 204237 at GULP1 225814 at XRN1 98.0 ··· 204237 at GULP1 244409 at CCDC154 98.0 ··· 217511 at KAZALD1 244409 at CCDC154 98.0 ··· 209262 s at NR2F6 244409 at CCDC154 98.0 ··· 201904 s at CTDSPL 244409 at CCDC154 98.0 ··· 233986 s at PLEKHG2 244409 at CCDC154 98.0 ··· 233986 s at PLEKHG2 214451 at TFAP2B 98.0 ··· 233986 s at PLEKHG2 1556606 at 0V2 98.0 ··· 233986 s at PLEKHG2 239132 at NOS1 98.0 ··· 241370 at LOC286052 233632 s at XRN1 98.0 ··· 241370 at LOC286052 225814 at XRN1 98.0 ··· 241370 at LOC286052 244409 at CCDC154 98.0 ··· 241370 at LOC286052 240911 at NOS1 98.0 ··· 209325 s at RGS16 244409 at CCDC154 98.0 ··· 202313 at PPP2R2A 244409 at CCDC154 98.0 ··· 235570 at RBMS3 244409 at CCDC154 98.0 ··· 209892 at FUT4 233632 s at XRN1 98.0 ··· 209892 at FUT4 225814 at XRN1 98.0 ··· 209892 at FUT4 244409 at CCDC154 98.0 ··· 204639 at ADA 244409 at CCDC154 98.0 ···

49 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 201772 at AZIN1 244409 at CCDC154 98.0 ··· 204163 at EMILIN1 225814 at XRN1 98.0 ··· 204163 at EMILIN1 244409 at CCDC154 98.0 ··· 202478 at TRIB2 233632 s at XRN1 98.0 ··· 202478 at TRIB2 244409 at CCDC154 98.0 ··· 206858 s at HOXC6 244409 at CCDC154 98.0 ··· 212665 at TIPARP 233632 s at XRN1 98.0 ··· 212665 at TIPARP 225814 at XRN1 98.0 ··· 212665 at TIPARP 244409 at CCDC154 98.0 ··· 202670 at MAP2K1 244409 at CCDC154 98.0 ··· 219319 at HIF3A 244409 at CCDC154 98.0 ··· 232021 at GXYLT1 244409 at CCDC154 98.0 ··· 232021 at GXYLT1 240911 at NOS1 98.0 ··· 210022 at PCGF1 244409 at CCDC154 98.0 ··· 227911 at ARHGAP28 244409 at CCDC154 98.0 ··· 232555 at CREB5 244409 at CCDC154 98.0 ··· 219779 at ZFHX4 244409 at CCDC154 98.0 ··· 218695 at EXOSC4 244409 at CCDC154 98.0 ··· 219299 at TRMT12 244409 at CCDC154 98.0 ··· 209568 s at RGL1 244409 at CCDC154 98.0 ··· 202894 at EPHB4 244409 at CCDC154 98.0 ··· 219103 at ASAP3 244409 at CCDC154 98.0 ··· 244414 at NA 207076 s at ASS1 98.0 ··· 244414 at NA 233632 s at XRN1 98.0 ··· 244414 at NA 225814 at XRN1 98.0 ··· 244414 at NA 244409 at CCDC154 98.0 ··· 244414 at NA 240911 at NOS1 98.0 ··· 218135 at ERGIC2 225814 at XRN1 98.0 ··· 218135 at ERGIC2 244409 at CCDC154 98.0 ··· 211121 s at DOK1 244409 at CCDC154 98.0 ··· 224206 x at MYNN 244409 at CCDC154 98.0 ··· 224206 x at MYNN 221605 s at PIPOX 98.0 ··· 239262 at NA 233632 s at XRN1 98.0 ··· 239262 at NA 225814 at XRN1 98.0 ··· 239262 at NA 244409 at CCDC154 98.0 ··· 239262 at NA 240911 at NOS1 98.0 ··· 229034 at SOBP 244409 at CCDC154 98.0 ··· 203737 s at PPRC1 244409 at CCDC154 98.0 ··· 237833 s at SNCAIP 244409 at CCDC154 98.0 ··· 232541 at NA 233632 s at XRN1 98.0 ··· 232541 at NA 225814 at XRN1 98.0 ··· 232541 at NA 244409 at CCDC154 98.0 ··· 232541 at NA 240911 at NOS1 98.0 ··· 217946 s at SAE1 244409 at CCDC154 98.0 ··· 212188 at KCTD12 233632 s at XRN1 98.0 ··· 212188 at KCTD12 244409 at CCDC154 98.0 ··· 209928 s at MSC 244409 at CCDC154 98.0 ··· 239604 at NA 244409 at CCDC154 98.0 ··· 239604 at NA 240911 at NOS1 98.0 ··· 239604 at NA 1556606 at 0V2 98.0 ··· 239604 at NA 221605 s at PIPOX 98.0 ··· 239604 at NA 231916 at NOS1 98.0 ··· 239604 at NA 239132 at NOS1 98.0 ··· 218245 at TSKU 244409 at CCDC154 98.0 ··· 228574 at TMTC2 233632 s at XRN1 98.0 ··· 228574 at TMTC2 244409 at CCDC154 98.0 ··· 228574 at TMTC2 240911 at NOS1 98.0 ··· 228574 at TMTC2 1556606 at 0V2 98.0 ··· 228574 at TMTC2 239132 at NOS1 98.0 ··· 204716 at CCDC6 244409 at CCDC154 98.0 ··· 208732 at RAB2A 244409 at CCDC154 98.0 ··· 202145 at LY6E 233632 s at XRN1 98.0 ··· 202145 at LY6E 244409 at CCDC154 98.0 ··· 234351 x at TRPS1 244409 at CCDC154 98.0 ··· 226582 at LOC400043 233632 s at XRN1 98.0 ··· 226582 at LOC400043 244409 at CCDC154 98.0 ··· 226582 at LOC400043 240911 at NOS1 98.0 ··· 226582 at LOC400043 239132 at NOS1 98.0 ···

50 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 205732 s at NCOA2 244409 at CCDC154 98.0 ··· 208767 s at LAPTM4B 244409 at CCDC154 98.0 ··· 230257 s at TSEN15 240911 at NOS1 98.0 ··· 209158 s at CYTH2 244409 at CCDC154 98.0 ··· 202758 s at RFXANK 244409 at CCDC154 98.0 ··· 224895 at YAP1 233632 s at XRN1 98.0 ··· 224895 at YAP1 225814 at XRN1 98.0 ··· 224895 at YAP1 244409 at CCDC154 98.0 ··· 221094 s at ELP3 244409 at CCDC154 98.0 ··· 221814 at GPR124 244409 at CCDC154 98.0 ··· 212448 at NEDD4L 225305 at SLC25A29 98.0 ··· 212448 at NEDD4L 225306 s at SLC25A29 98.0 ··· 212448 at NEDD4L 244409 at CCDC154 98.0 ··· 218777 at REEP4 244409 at CCDC154 98.0 ··· 222155 s at SLC52A2 244409 at CCDC154 98.0 ··· 222155 s at SLC52A2 240911 at NOS1 98.0 ··· 222155 s at SLC52A2 239132 at NOS1 98.0 ··· 213345 at NFATC4 244409 at CCDC154 98.0 ··· 209247 s at ABCF2 244409 at CCDC154 98.0 ··· 213479 at NPTX2 244409 at CCDC154 98.0 ··· 206745 at HOXC11 244409 at CCDC154 98.0 ··· 212181 s at NA 244409 at CCDC154 98.0 ··· 212181 s at NA 240911 at NOS1 98.0 ··· 222551 s at C8orf33 244409 at CCDC154 98.0 ··· 227046 at SLC39A11 244409 at CCDC154 98.0 ··· 227046 at SLC39A11 240911 at NOS1 98.0 ··· 228882 at TUB 244409 at CCDC154 98.0 ··· 201827 at SMARCD2 244409 at CCDC154 98.0 ··· 206147 x at SCML2 244409 at CCDC154 98.0 ··· 222543 at DERL1 244409 at CCDC154 98.0 ··· 226038 at LONRF1 244409 at CCDC154 98.0 ··· 226038 at LONRF1 240911 at NOS1 98.0 ··· 226038 at LONRF1 1556606 at 0V2 98.0 ··· 226038 at LONRF1 221605 s at PIPOX 98.0 ··· 226038 at LONRF1 239132 at NOS1 98.0 ··· 47560 at LPHN1 244409 at CCDC154 98.0 ··· 203643 at ERF 244409 at CCDC154 98.0 ··· 220941 s at C21orf91 244409 at CCDC154 98.0 ··· 203119 at CCDC86 244409 at CCDC154 98.0 ··· 226294 x at FAM91A1 244409 at CCDC154 98.0 ··· 226294 x at FAM91A1 240911 at NOS1 98.0 ··· 226294 x at FAM91A1 239132 at NOS1 98.0 ··· 44783 s at HEY1 244409 at CCDC154 98.0 ··· 208712 at CCND1 233632 s at XRN1 98.0 ··· 208712 at CCND1 225814 at XRN1 98.0 ··· 208712 at CCND1 244409 at CCDC154 98.0 ··· 204849 at TCFL5 244409 at CCDC154 98.0 ··· 206805 at SEMA3A 244409 at CCDC154 98.0 ··· 215690 x at GPAA1 244409 at CCDC154 98.0 ··· 219124 at TTI2 244409 at CCDC154 98.0 ··· 219124 at TTI2 240911 at NOS1 98.0 ··· 219124 at TTI2 1556606 at 0V2 98.0 ··· 219124 at TTI2 231916 at NOS1 98.0 ··· 219124 at TTI2 239132 at NOS1 98.0 ··· 227410 at FAM43A 244409 at CCDC154 98.0 ··· 227410 at FAM43A 240911 at NOS1 98.0 ··· 218961 s at PNKP 244409 at CCDC154 98.0 ··· 243932 at NA 225814 at XRN1 98.0 ··· 243932 at NA 244409 at CCDC154 98.0 ··· 243932 at NA 240911 at NOS1 98.0 ··· 243932 at NA 239132 at NOS1 98.0 ··· 214873 at LRP5L 244409 at CCDC154 98.0 ··· 231056 at LOC339352 244409 at CCDC154 98.0 ··· 231056 at LOC339352 240911 at NOS1 98.0 ··· 222757 s at ZAK 244409 at CCDC154 98.0 ··· 201870 at TOMM34 244409 at CCDC154 98.0 ··· 212563 at BOP1 244409 at CCDC154 98.0 ··· 212563 at BOP1 240911 at NOS1 98.0 ···

51 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 210380 s at CAC01G 244409 at CCDC154 98.0 ··· 204014 at DUSP4 244409 at CCDC154 98.0 ··· 202657 s at SERTAD2 244409 at CCDC154 98.0 ··· 209324 s at RGS16 244409 at CCDC154 98.0 ··· 213891 s at TCF4 244409 at CCDC154 98.0 ··· 208713 at HNRNPUL1 244409 at CCDC154 98.0 ··· 222236 s at ASAP3 244409 at CCDC154 98.0 ··· 205372 at PLAG1 244409 at CCDC154 98.0 ··· 229632 s at INTS10 244409 at CCDC154 98.0 ··· 229632 s at INTS10 240911 at NOS1 98.0 ··· 229632 s at INTS10 1556606 at 0V2 98.0 ··· 229632 s at INTS10 231916 at NOS1 98.0 ··· 229632 s at INTS10 239132 at NOS1 98.0 ··· 219774 at CCDC93 244409 at CCDC154 98.0 ··· 202814 s at HEXIM1 233632 s at XRN1 98.0 ··· 202814 s at HEXIM1 244409 at CCDC154 98.0 ··· 231784 s at DCAF13 244409 at CCDC154 98.0 ··· 211060 x at GPAA1 244409 at CCDC154 98.0 ··· 201639 s at CPSF1 244409 at CCDC154 98.0 ··· 209567 at RRS1 244409 at CCDC154 98.0 ··· 223569 at PPAPDC1B 233632 s at XRN1 98.0 ··· 223569 at PPAPDC1B 225814 at XRN1 98.0 ··· 223569 at PPAPDC1B 244409 at CCDC154 98.0 ··· 223569 at PPAPDC1B 240911 at NOS1 98.0 ··· 223569 at PPAPDC1B 1556606 at 0V2 98.0 ··· 223569 at PPAPDC1B 221605 s at PIPOX 98.0 ··· 223569 at PPAPDC1B 239132 at NOS1 98.0 ··· 212385 at TCF4 233632 s at XRN1 98.0 ··· 212385 at TCF4 244409 at CCDC154 98.0 ··· 201126 s at MGAT1 233632 s at XRN1 98.0 ··· 201126 s at MGAT1 225814 at XRN1 98.0 ··· 201126 s at MGAT1 244409 at CCDC154 98.0 ··· 231872 at LRRCC1 244409 at CCDC154 98.0 ··· 231872 at LRRCC1 240911 at NOS1 98.0 ··· 231872 at LRRCC1 1556606 at 0V2 98.0 ··· 231872 at LRRCC1 239132 at NOS1 98.0 ··· 212256 at GALNT10 233632 s at XRN1 98.0 ··· 212256 at GALNT10 225814 at XRN1 98.0 ··· 212256 at GALNT10 244409 at CCDC154 98.0 ··· 229377 at GRTP1 244409 at CCDC154 98.0 ··· 33132 at CPSF1 244409 at CCDC154 98.0 ··· 235664 at NA 225305 at SLC25A29 98.0 ··· 235664 at NA 225306 s at SLC25A29 98.0 ··· 235664 at NA 244409 at CCDC154 98.0 ··· 235664 at NA 240911 at NOS1 98.0 ··· 202747 s at ITM2A 244409 at CCDC154 98.0 ··· 226150 at PPAPDC1B 225814 at XRN1 98.0 ··· 226150 at PPAPDC1B 244409 at CCDC154 98.0 ··· 226150 at PPAPDC1B 240911 at NOS1 98.0 ··· 226150 at PPAPDC1B 239132 at NOS1 98.0 ··· 201985 at KIAA0196 244409 at CCDC154 98.0 ··· 238045 at TMEM65 244409 at CCDC154 98.0 ··· 238045 at TMEM65 240911 at NOS1 98.0 ··· 212248 at MTDH 244409 at CCDC154 98.0 ··· 1569025 s at FAM13A 233632 s at XRN1 98.0 ··· 1569025 s at FAM13A 244409 at CCDC154 98.0 ··· 229067 at SRGAP2P1 244409 at CCDC154 98.0 ··· 229067 at SRGAP2P1 240911 at NOS1 98.0 ··· 229067 at SRGAP2P1 231916 at NOS1 98.0 ··· 229067 at SRGAP2P1 239132 at NOS1 98.0 ··· 217792 at SNX5 244409 at CCDC154 98.0 ··· 200707 at PRKCSH 244409 at CCDC154 98.0 ··· 221807 s at TRABD 244409 at CCDC154 98.0 ··· 230163 at GFRA1 233632 s at XRN1 98.0 ··· 230163 at GFRA1 244409 at CCDC154 98.0 ··· 219072 at BCL7C 244409 at CCDC154 98.0 ··· 208689 s at RPN2 244409 at CCDC154 98.0 ··· 226974 at NEDD4L 233632 s at XRN1 98.0 ···

52 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 226974 at NEDD4L 225814 at XRN1 98.0 ··· 226974 at NEDD4L 244409 at CCDC154 98.0 ··· 227100 at B3GALTL 226576 at ARHGAP26 98.0 ··· 227100 at B3GALTL 244409 at CCDC154 98.0 ··· 227100 at B3GALTL 240911 at NOS1 98.0 ··· 227100 at B3GALTL 230076 at PITPNM3 98.0 ··· 227100 at B3GALTL 231916 at NOS1 98.0 ··· 227100 at B3GALTL 239132 at NOS1 98.0 ··· 204038 s at LPAR1 244409 at CCDC154 98.0 ··· 203870 at USP46 244409 at CCDC154 98.0 ··· 208361 s at POLR3D 244409 at CCDC154 98.0 ··· 229172 at HSPA12B 244409 at CCDC154 98.0 ··· 229172 at HSPA12B 240911 at NOS1 98.0 ··· 226349 at C12orf45 244409 at CCDC154 98.0 ··· 202134 s at WWTR1 244409 at CCDC154 98.0 ··· 212885 at MPHOSPH10 244409 at CCDC154 98.0 ··· 212814 at AHCYL2 233632 s at XRN1 98.0 ··· 212814 at AHCYL2 244409 at CCDC154 98.0 ··· 205047 s at ASNS 244409 at CCDC154 98.0 ··· 222701 s at CHCHD7 233632 s at XRN1 98.0 ··· 222701 s at CHCHD7 225814 at XRN1 98.0 ··· 222701 s at CHCHD7 244409 at CCDC154 98.0 ··· 200970 s at SERP1 244409 at CCDC154 98.0 ··· 212356 at KHNYN 233632 s at XRN1 98.0 ··· 212356 at KHNYN 244409 at CCDC154 98.0 ··· 205731 s at NCOA2 244409 at CCDC154 98.0 ··· 231764 at CHRAC1 244409 at CCDC154 98.0 ··· 231764 at CHRAC1 240911 at NOS1 98.0 ··· 231764 at CHRAC1 1556606 at 0V2 98.0 ··· 231764 at CHRAC1 221605 s at PIPOX 98.0 ··· 206739 at HOXC5 244409 at CCDC154 98.0 ··· 202701 at BMP1 244409 at CCDC154 98.0 ··· 201252 at PSMC4 244409 at CCDC154 98.0 ··· 228082 at CLMP 244409 at CCDC154 98.0 ··· 228082 at CLMP 240911 at NOS1 98.0 ··· 209253 at SORBS3 244409 at CCDC154 98.0 ··· 219402 s at DERL1 244409 at CCDC154 98.0 ··· 220326 s at ARHGEF40 233632 s at XRN1 98.0 ··· 220326 s at ARHGEF40 244409 at CCDC154 98.0 ··· 220326 s at ARHGEF40 240911 at NOS1 98.0 ··· 208734 x at RAB2A 244409 at CCDC154 98.0 ··· 1555358 a at ENTPD4 244409 at CCDC154 98.0 ··· 232333 at NA 207076 s at ASS1 98.0 ··· 232333 at NA 233632 s at XRN1 98.0 ··· 232333 at NA 225814 at XRN1 98.0 ··· 232333 at NA 244409 at CCDC154 98.0 ··· 232333 at NA 240911 at NOS1 98.0 ··· 1555997 s at IGFBP5 244409 at CCDC154 98.0 ··· 1558569 at LOC100131541 233632 s at XRN1 98.0 ··· 1558569 at LOC100131541 225814 at XRN1 98.0 ··· 1558569 at LOC100131541 244409 at CCDC154 98.0 ··· 1558569 at LOC100131541 240911 at NOS1 98.0 ··· 1552337 s at HOXD4 244409 at CCDC154 98.0 ··· 1552337 s at HOXD4 221605 s at PIPOX 98.0 ··· 211126 s at CSRP2 244409 at CCDC154 98.0 ··· 203534 at LSM1 244409 at CCDC154 98.0 ··· 1559796 at EBF3 244409 at CCDC154 98.0 ··· 1559796 at EBF3 240911 at NOS1 98.0 ··· 208029 s at LAPTM4B 244409 at CCDC154 98.0 ··· 202800 at SLC1A3 244409 at CCDC154 98.0 ··· 204086 at PRAME 244409 at CCDC154 98.0 ··· 212355 at KHNYN 233632 s at XRN1 98.0 ··· 212355 at KHNYN 244409 at CCDC154 98.0 ··· 203425 s at IGFBP5 244409 at CCDC154 98.0 ··· 200076 s at KXD1 244409 at CCDC154 98.0 ··· 200076 s at KXD1 240911 at NOS1 98.0 ··· 209406 at BAG2 225814 at XRN1 98.0 ··· 209406 at BAG2 244409 at CCDC154 98.0 ···

53 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 223216 x at ZNF395 244409 at CCDC154 98.0 ··· 219071 x at FAM203A 244409 at CCDC154 98.0 ··· 219071 x at FAM203A 240911 at NOS1 98.0 ··· 219863 at HERC5 244409 at CCDC154 98.0 ··· 1554679 a at LAPTM4B 244409 at CCDC154 98.0 ··· 221810 at RAB15 244409 at CCDC154 98.0 ··· 204175 at ZNF593 244409 at CCDC154 98.0 ··· 204976 s at AMMECR1 233632 s at XRN1 98.0 ··· 204976 s at AMMECR1 244409 at CCDC154 98.0 ··· 214039 s at LAPTM4B 244409 at CCDC154 98.0 ··· 205375 at MDFI 244409 at CCDC154 98.0 ··· 201480 s at SUPT5H 244409 at CCDC154 98.0 ··· 213399 x at RPN2 244409 at CCDC154 98.0 ··· 234645 at NA 233632 s at XRN1 98.0 ··· 234645 at NA 244409 at CCDC154 98.0 ··· 234645 at NA 240911 at NOS1 98.0 ··· 219550 at ROBO3 244409 at CCDC154 98.0 ··· 213151 s at 7-Sep 244409 at CCDC154 98.0 ··· 213151 s at 7-Sep 240911 at NOS1 98.0 ··· 223435 s at NA 244409 at CCDC154 98.0 ··· 223435 s at NA 240911 at NOS1 98.0 ··· 223435 s at NA 230076 at PITPNM3 98.0 ··· 223435 s at NA 1556606 at 0V2 98.0 ··· 223435 s at NA 221605 s at PIPOX 98.0 ··· 223435 s at NA 239132 at NOS1 98.0 ··· 208060 at PAX7 244409 at CCDC154 98.0 ··· 200617 at MLEC 244409 at CCDC154 98.0 ··· 219755 at CBX8 244409 at CCDC154 98.0 ··· 208546 x at HIST1H2BH 244409 at CCDC154 98.0 ··· 219039 at SEMA4C 244409 at CCDC154 98.0 ··· 235018 at CSRNP3 206447 at NA 98.0 ··· 235018 at CSRNP3 206446 s at NA 98.0 ··· 235018 at CSRNP3 244409 at CCDC154 98.0 ··· 210950 s at FDFT1 244409 at CCDC154 98.0 ··· 218070 s at GMPPA 244409 at CCDC154 98.0 ··· 202734 at TRIP10 244409 at CCDC154 98.0 ··· 212793 at DAAM2 233632 s at XRN1 98.0 ··· 212793 at DAAM2 244409 at CCDC154 98.0 ··· 238323 at TEAD2 244409 at CCDC154 98.0 ··· 238323 at TEAD2 240911 at NOS1 98.0 ··· 221004 s at ITM2C 244409 at CCDC154 98.0 ··· 234983 at NA 244409 at CCDC154 98.0 ··· 234983 at NA 240911 at NOS1 98.0 ··· 234983 at NA 239132 at NOS1 98.0 ··· 235459 at RNF41 244409 at CCDC154 98.0 ··· 219682 s at TBX3 225814 at XRN1 98.0 ··· 219682 s at TBX3 244409 at CCDC154 98.0 ··· 228141 at GPX8 233632 s at XRN1 98.0 ··· 228141 at GPX8 244409 at CCDC154 98.0 ··· 228141 at GPX8 240911 at NOS1 98.0 ··· 228141 at GPX8 214451 at TFAP2B 98.0 ··· 229493 at HOXD-AS2 244409 at CCDC154 98.0 ··· 229493 at HOXD-AS2 240911 at NOS1 98.0 ··· 229493 at HOXD-AS2 239132 at NOS1 98.0 ··· 213170 at GPX7 244409 at CCDC154 98.0 ··· 202924 s at PLAGL2 244409 at CCDC154 98.0 ··· 223689 at IGF2BP1 244409 at CCDC154 98.0 ··· 223689 at IGF2BP1 240911 at NOS1 98.0 ··· 214431 at GMPS 244409 at CCDC154 98.0 ··· 222692 s at FNDC3B 233632 s at XRN1 98.0 ··· 222692 s at FNDC3B 225814 at XRN1 98.0 ··· 222692 s at FNDC3B 244409 at CCDC154 98.0 ··· 236115 at HTR7P1 233632 s at XRN1 98.0 ··· 236115 at HTR7P1 244409 at CCDC154 98.0 ··· 236115 at HTR7P1 240911 at NOS1 98.0 ··· 231832 at NA 244409 at CCDC154 98.0 ··· 231832 at NA 240911 at NOS1 98.0 ··· 218278 at WDR74 244409 at CCDC154 98.0 ···

54 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 201718 s at EPB41L2 244409 at CCDC154 98.0 ··· 225842 at PHLDA1 244409 at CCDC154 98.0 ··· 217899 at TMEM214 225814 at XRN1 98.0 ··· 217899 at TMEM214 244409 at CCDC154 98.0 ··· 200062 s at RPL30 244409 at CCDC154 98.0 ··· 218337 at FAM160B2 244409 at CCDC154 98.0 ··· 221019 s at COLEC12 233632 s at XRN1 98.0 ··· 221019 s at COLEC12 225814 at XRN1 98.0 ··· 221019 s at COLEC12 244409 at CCDC154 98.0 ··· 218000 s at PHLDA1 244409 at CCDC154 98.0 ··· 201566 x at ID2 244409 at CCDC154 98.0 ··· 208642 s at XRCC5 231580 at LOC100506542 98.0 ··· 208642 s at XRCC5 244409 at CCDC154 98.0 ··· 211432 s at TYRO3 244409 at CCDC154 98.0 ··· 218426 s at RNF216 244409 at CCDC154 98.0 ··· 205204 at NMB 244409 at CCDC154 98.0 ··· 205135 s at NUFIP1 244409 at CCDC154 98.0 ··· 232352 at ISL2 206446 s at NA 98.0 ··· 232352 at ISL2 244409 at CCDC154 98.0 ··· 232352 at ISL2 240911 at NOS1 98.0 ··· 232352 at ISL2 231916 at NOS1 98.0 ··· 232352 at ISL2 239132 at NOS1 98.0 ··· 228791 at LOC100129502 244409 at CCDC154 98.0 ··· 201906 s at CTDSPL 244409 at CCDC154 98.0 ··· 205376 at INPP4B 225814 at XRN1 98.0 ··· 205376 at INPP4B 244409 at CCDC154 98.0 ··· 203088 at FBLN5 244409 at CCDC154 98.0 ··· 201565 s at ID2 233632 s at XRN1 98.0 ··· 201565 s at ID2 244409 at CCDC154 98.0 ··· 218159 at DDRGK1 244409 at CCDC154 98.0 ··· 217997 at PHLDA1 244409 at CCDC154 98.0 ··· 219825 at CYP26B1 233632 s at XRN1 98.0 ··· 219825 at CYP26B1 225814 at XRN1 98.0 ··· 219825 at CYP26B1 244409 at CCDC154 98.0 ··· 208113 x at PABPC3 244409 at CCDC154 98.0 ··· 223126 s at C1orf21 244409 at CCDC154 98.0 ··· 212713 at MFAP4 244409 at CCDC154 98.0 ··· 205151 s at TRIL 244409 at CCDC154 98.0 ··· 229952 at NA 244409 at CCDC154 98.0 ··· 229952 at NA 240911 at NOS1 98.0 ··· 236896 at ZIC1 233632 s at XRN1 98.0 ··· 236896 at ZIC1 244409 at CCDC154 98.0 ··· 239466 at LOC344595 223974 at MGC11082 98.0 ··· 239466 at LOC344595 244409 at CCDC154 98.0 ··· 239466 at LOC344595 240911 at NOS1 98.0 ··· 239466 at LOC344595 230076 at PITPNM3 98.0 ··· 239466 at LOC344595 239132 at NOS1 98.0 ··· 201204 s at RRBP1 233632 s at XRN1 98.0 ··· 201204 s at RRBP1 225814 at XRN1 98.0 ··· 201204 s at RRBP1 244409 at CCDC154 98.0 ··· 59697 at RAB15 244409 at CCDC154 98.0 ··· 225600 at C8orf83 244409 at CCDC154 98.0 ··· 225600 at C8orf83 240911 at NOS1 98.0 ··· 225600 at C8orf83 230076 at PITPNM3 98.0 ··· 225600 at C8orf83 231916 at NOS1 98.0 ··· 225600 at C8orf83 239132 at NOS1 98.0 ··· 232716 at NA 233632 s at XRN1 98.0 ··· 232716 at NA 244409 at CCDC154 98.0 ··· 232716 at NA 240911 at NOS1 98.0 ··· 204239 s at N0T 244409 at CCDC154 98.0 ··· 208639 x at PDIA6 238432 at FLJ35776 98.0 ··· 208639 x at PDIA6 244409 at CCDC154 98.0 ··· 227377 at IGF2BP1 244409 at CCDC154 98.0 ··· 227377 at IGF2BP1 240911 at NOS1 98.0 ··· 227377 at IGF2BP1 239132 at NOS1 98.0 ··· 202906 s at NBN 233632 s at XRN1 98.0 ··· 202906 s at NBN 225814 at XRN1 98.0 ··· 202906 s at NBN 244409 at CCDC154 98.0 ···

55 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 223842 s at SCARA3 244409 at CCDC154 98.0 ··· 224807 at GRAMD1A 244409 at CCDC154 98.0 ··· 224807 at GRAMD1A 240911 at NOS1 98.0 ··· 202656 s at SERTAD2 244409 at CCDC154 98.0 ··· 205931 s at CREB5 244409 at CCDC154 98.0 ··· 218499 at MST4 244409 at CCDC154 98.0 ··· 218499 at MST4 240911 at NOS1 98.0 ··· 218499 at MST4 239132 at NOS1 98.0 ··· 1554697 at ADAMTS9 244409 at CCDC154 98.0 ··· 244007 at ZNF462 244409 at CCDC154 98.0 ··· 244007 at ZNF462 240911 at NOS1 98.0 ··· 201369 s at ZFP36L2 244409 at CCDC154 98.0 ··· 222917 s at TBX3 244409 at CCDC154 98.0 ··· 222411 s at SSR3 244409 at CCDC154 98.0 ··· 211958 at IGFBP5 244409 at CCDC154 98.0 ··· 225203 at PPP1R16A 244409 at CCDC154 98.0 ··· 225203 at PPP1R16A 240911 at NOS1 98.0 ··· 225203 at PPP1R16A 1556606 at 0V2 98.0 ··· 225203 at PPP1R16A 221605 s at PIPOX 98.0 ··· 225203 at PPP1R16A 231916 at NOS1 98.0 ··· 225203 at PPP1R16A 239132 at NOS1 98.0 ··· 229281 at NPAS3 244409 at CCDC154 98.0 ··· 210628 x at LTBP4 244409 at CCDC154 98.0 ··· 212850 s at LRP4 244409 at CCDC154 98.0 ··· 201203 s at RRBP1 244409 at CCDC154 98.0 ··· 239984 at NA 244409 at CCDC154 98.0 ··· 239984 at NA 240911 at NOS1 98.0 ··· 232693 s at NA 244409 at CCDC154 98.0 ··· 232693 s at NA 240911 at NOS1 98.0 ··· 232693 s at NA 239132 at NOS1 98.0 ··· 219416 at SCARA3 244409 at CCDC154 98.0 ··· 226710 at C8orf82 244409 at CCDC154 98.0 ··· 226710 at C8orf82 240911 at NOS1 98.0 ··· 226710 at C8orf82 1556606 at 0V2 98.0 ··· 226710 at C8orf82 221605 s at PIPOX 98.0 ··· 226710 at C8orf82 239132 at NOS1 98.0 ··· 200936 at RPL8 244409 at CCDC154 98.0 ··· 1558775 s at NSMAF 244409 at CCDC154 98.0 ··· 200619 at SF3B2 244409 at CCDC154 98.0 ··· 228065 at BCL9L 244409 at CCDC154 98.0 ··· 228065 at BCL9L 240911 at NOS1 98.0 ··· 216835 s at DOK1 244409 at CCDC154 98.0 ··· 208658 at PDIA4 244409 at CCDC154 98.0 ··· 236852 at FBXO43 244409 at CCDC154 98.0 ··· 236852 at FBXO43 240911 at NOS1 98.0 ··· 236852 at FBXO43 1556606 at 0V2 98.0 ··· 236852 at FBXO43 231916 at NOS1 98.0 ··· 236852 at FBXO43 239132 at NOS1 98.0 ··· 201433 s at PTDSS1 244409 at CCDC154 98.0 ··· 208731 at RAB2A 244409 at CCDC154 98.0 ··· 225402 at TP53RK 244409 at CCDC154 98.0 ··· 225402 at TP53RK 240911 at NOS1 98.0 ··· 203228 at PAFAH1B3 244409 at CCDC154 98.0 ··· 218151 x at SLC52A2 244409 at CCDC154 98.0 ··· 218151 x at SLC52A2 240911 at NOS1 98.0 ··· 242405 at NA 233632 s at XRN1 98.0 ··· 242405 at NA 225814 at XRN1 98.0 ··· 242405 at NA 244409 at CCDC154 98.0 ··· 242405 at NA 240911 at NOS1 98.0 ··· 203424 s at IGFBP5 244409 at CCDC154 98.0 ··· 215823 x at NA 244409 at CCDC154 98.0 ··· 215823 x at NA 240911 at NOS1 98.0 ··· 209592 s at DCAF7 244409 at CCDC154 98.0 ··· 227684 at S1PR2 244409 at CCDC154 98.0 ··· 201399 s at TRAM1 244409 at CCDC154 98.0 ··· 205116 at LAMA2 244409 at CCDC154 98.0 ··· 238322 s at TEAD2 244409 at CCDC154 98.0 ··· 238322 s at TEAD2 240911 at NOS1 98.0 ···

56 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 229568 at MOB3B 244409 at CCDC154 98.0 ··· 229568 at MOB3B 240911 at NOS1 98.0 ··· 229568 at MOB3B 221605 s at PIPOX 98.0 ··· 231382 at FGF18 244409 at CCDC154 98.0 ··· 216305 s at GCFC2 244409 at CCDC154 98.0 ··· 216305 s at GCFC2 240911 at NOS1 98.0 ··· 216305 s at GCFC2 239132 at NOS1 98.0 ··· 222572 at PDP1 244409 at CCDC154 98.0 ··· 219145 at LPHN1 244409 at CCDC154 98.0 ··· 209453 at SLC9A1 244409 at CCDC154 98.0 ··· 226691 at TNRC18 225305 at SLC25A29 98.0 ··· 226691 at TNRC18 244409 at CCDC154 98.0 ··· 226691 at TNRC18 240911 at NOS1 98.0 ··· 225133 at KLF3 233632 s at XRN1 98.0 ··· 225133 at KLF3 244409 at CCDC154 98.0 ··· 201745 at TWF1 244409 at CCDC154 98.0 ··· 213564 x at LDHB 225814 at XRN1 98.0 ··· 213564 x at LDHB 244409 at CCDC154 98.0 ··· 225835 at SLC12A2 233632 s at XRN1 98.0 ··· 225835 at SLC12A2 244409 at CCDC154 98.0 ··· 225399 at TSEN15 244409 at CCDC154 98.0 ··· 225399 at TSEN15 240911 at NOS1 98.0 ··· 225399 at TSEN15 221605 s at PIPOX 98.0 ··· 225399 at TSEN15 239132 at NOS1 98.0 ··· 207357 s at GALNT10 244409 at CCDC154 98.0 ··· 209384 at PROSC 244409 at CCDC154 98.0 ··· 209516 at SMYD5 244409 at CCDC154 98.0 ··· 209899 s at PUF60 244409 at CCDC154 98.0 ··· 242137 at RBMS3 244409 at CCDC154 98.0 ··· 212386 at TCF4 244409 at CCDC154 98.0 ··· 235684 s at SESN3 206446 s at NA 98.0 ··· 235684 s at SESN3 244409 at CCDC154 98.0 ··· 235684 s at SESN3 240911 at NOS1 98.0 ··· 235684 s at SESN3 230076 at PITPNM3 98.0 ··· 235684 s at SESN3 1556606 at 0V2 98.0 ··· 235684 s at SESN3 221605 s at PIPOX 98.0 ··· 235684 s at SESN3 231916 at NOS1 98.0 ··· 235684 s at SESN3 239132 at NOS1 98.0 ··· 202746 at ITM2A 244409 at CCDC154 98.0 ··· 224407 s at MST4 244409 at CCDC154 98.0 ··· 224407 s at MST4 240911 at NOS1 98.0 ··· 224407 s at MST4 239132 at NOS1 98.0 ··· 216640 s at PDIA6 238432 at FLJ35776 98.0 ··· 216640 s at PDIA6 244409 at CCDC154 98.0 ··· 216749 at NA 244409 at CCDC154 98.0 ··· 216749 at NA 240911 at NOS1 98.0 ··· 218482 at ENY2 244409 at CCDC154 98.0 ··· 65718 at GPR124 233632 s at XRN1 98.0 ··· 65718 at GPR124 225814 at XRN1 98.0 ··· 65718 at GPR124 244409 at CCDC154 98.0 ··· 208837 at TMED3 244409 at CCDC154 98.0 ··· 235606 at LOC344595 244409 at CCDC154 98.0 ··· 235606 at LOC344595 240911 at NOS1 98.0 ··· 244246 at MIPOL1 244409 at CCDC154 98.0 ··· 244246 at MIPOL1 240911 at NOS1 98.0 ··· 244246 at MIPOL1 1556606 at 0V2 98.0 ··· 244246 at MIPOL1 221605 s at PIPOX 98.0 ··· 244246 at MIPOL1 239132 at NOS1 98.0 ··· 213176 s at LTBP4 244409 at CCDC154 98.0 ··· 217299 s at NBN 233632 s at XRN1 98.0 ··· 217299 s at NBN 225814 at XRN1 98.0 ··· 217299 s at NBN 244409 at CCDC154 98.0 ··· 221845 s at CLPB 244409 at CCDC154 98.0 ··· 201764 at TMEM106C 244409 at CCDC154 98.0 ··· 232051 at CCDC102A 244409 at CCDC154 98.0 ··· 232051 at CCDC102A 240911 at NOS1 98.0 ··· 232051 at CCDC102A 1556606 at 0V2 98.0 ··· 232051 at CCDC102A 221605 s at PIPOX 98.0 ···

57 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 232051 at CCDC102A 231916 at NOS1 98.0 ··· 232051 at CCDC102A 239132 at NOS1 98.0 ··· 222998 at MAF1 244409 at CCDC154 98.0 ··· 222998 at MAF1 240911 at NOS1 98.0 ··· 222998 at MAF1 221605 s at PIPOX 98.0 ··· 222998 at MAF1 239132 at NOS1 98.0 ··· 213243 at VPS13B 225814 at XRN1 98.0 ··· 213243 at VPS13B 1553394 a at TFAP2B 98.0 ··· 213243 at VPS13B 244409 at CCDC154 98.0 ··· 205240 at GPSM2 244409 at CCDC154 98.0 ··· 205150 s at TRIL 244409 at CCDC154 98.0 ··· 205228 at RBMS2 244409 at CCDC154 98.0 ··· 218388 at PGLS 244409 at CCDC154 98.0 ··· 58696 at EXOSC4 244409 at CCDC154 98.0 ··· 224776 at AGPAT6 244409 at CCDC154 98.0 ··· 224776 at AGPAT6 240911 at NOS1 98.0 ··· 224776 at AGPAT6 1556606 at 0V2 98.0 ··· 224776 at AGPAT6 221605 s at PIPOX 98.0 ··· 224776 at AGPAT6 239132 at NOS1 98.0 ··· 224947 at RNF26 244409 at CCDC154 98.0 ··· 224947 at RNF26 240911 at NOS1 98.0 ··· 224947 at RNF26 1556606 at 0V2 98.0 ··· 224947 at RNF26 221605 s at PIPOX 98.0 ··· 224947 at RNF26 239132 at NOS1 98.0 ··· 209043 at PAPSS1 244409 at CCDC154 98.0 ··· 219418 at NHEJ1 244409 at CCDC154 98.0 ··· 218629 at SMO 244409 at CCDC154 98.0 ··· 204724 s at COL9A3 244409 at CCDC154 98.0 ··· 224894 at YAP1 233632 s at XRN1 98.0 ··· 224894 at YAP1 225814 at XRN1 98.0 ··· 224894 at YAP1 244409 at CCDC154 98.0 ··· 213491 x at RPN2 244409 at CCDC154 98.0 ··· 207595 s at BMP1 244409 at CCDC154 98.0 ··· 221836 s at TRAPPC9 244409 at CCDC154 98.0 ··· 218387 s at PGLS 244409 at CCDC154 98.0 ··· 220890 s at DDX47 244409 at CCDC154 98.0 ··· 238004 at PGBD2 1553394 a at TFAP2B 98.0 ··· 238004 at PGBD2 244409 at CCDC154 98.0 ··· 238004 at PGBD2 240911 at NOS1 98.0 ··· 238004 at PGBD2 230076 at PITPNM3 98.0 ··· 238004 at PGBD2 221605 s at PIPOX 98.0 ··· 238004 at PGBD2 239132 at NOS1 98.0 ··· 232776 at NA 244409 at CCDC154 98.0 ··· 232776 at NA 240911 at NOS1 98.0 ··· 232776 at NA 214451 at TFAP2B 98.0 ··· 232776 at NA 239132 at NOS1 98.0 ··· 222206 s at NCLN 244409 at CCDC154 98.0 ··· 202639 s at RANBP3 244409 at CCDC154 98.0 ··· 209545 s at RIPK2 244409 at CCDC154 98.0 ··· 228977 at LOC729680 244409 at CCDC154 98.0 ··· 228977 at LOC729680 240911 at NOS1 98.0 ··· 228977 at LOC729680 221605 s at PIPOX 98.0 ··· 221802 s at KIAA1598 244409 at CCDC154 98.0 ··· 1562588 at NA 244409 at CCDC154 98.0 ··· 1562588 at NA 240911 at NOS1 98.0 ··· 1562588 at NA 221605 s at PIPOX 98.0 ··· 1562588 at NA 231916 at NOS1 98.0 ··· 1562588 at NA 239132 at NOS1 98.0 ··· 207790 at LRRC1 244409 at CCDC154 98.0 ··· 219832 s at HOXC13 244409 at CCDC154 98.0 ··· 226021 at RDH10 233632 s at XRN1 98.0 ··· 226021 at RDH10 244409 at CCDC154 98.0 ··· 226021 at RDH10 240911 at NOS1 98.0 ··· 242887 at KCMF1 244409 at CCDC154 98.0 ··· 218059 at ZNF706 244409 at CCDC154 98.0 ··· 228504 at SCN7A 244409 at CCDC154 98.0 ··· 1552572 a at MIPOL1 244409 at CCDC154 98.0 ··· 1552572 a at MIPOL1 240911 at NOS1 98.0 ···

58 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 1552572 a at MIPOL1 221605 s at PIPOX 98.0 ··· 203616 at POLB 244409 at CCDC154 98.0 ··· 205667 at WRN 244409 at CCDC154 98.0 ··· 1552946 at ZNF114 244409 at CCDC154 98.0 ··· 1552946 at ZNF114 240911 at NOS1 98.0 ··· 1552946 at ZNF114 1556606 at 0V2 98.0 ··· 1552946 at ZNF114 221605 s at PIPOX 98.0 ··· 1552946 at ZNF114 231916 at NOS1 98.0 ··· 222335 at NA 244409 at CCDC154 98.0 ··· 222335 at NA 240911 at NOS1 98.0 ··· 222335 at NA 231916 at NOS1 98.0 ··· 213554 s at CDV3 244409 at CCDC154 98.0 ··· 225163 at FRMD4A 244409 at CCDC154 98.0 ··· 241122 s at MUSK 244409 at CCDC154 98.0 ··· 204073 s at C11orf9 244409 at CCDC154 98.0 ··· 218823 s at KCTD9 244409 at CCDC154 98.0 ··· 65588 at LOC388796 244409 at CCDC154 98.0 ··· 226844 at MOB3B 244409 at CCDC154 98.0 ··· 226844 at MOB3B 240911 at NOS1 98.0 ··· 203071 at SEMA3B 244409 at CCDC154 98.0 ··· 235205 at OXR1 244409 at CCDC154 98.0 ··· 226408 at TEAD2 233632 s at XRN1 98.0 ··· 226408 at TEAD2 225814 at XRN1 98.0 ··· 226408 at TEAD2 244409 at CCDC154 98.0 ··· 226408 at TEAD2 240911 at NOS1 98.0 ··· 213848 at DUSP7 244409 at CCDC154 98.0 ··· 201652 at COPS5 244409 at CCDC154 98.0 ··· 207622 s at ABCF2 244409 at CCDC154 98.0 ··· 202875 s at PBX2 244409 at CCDC154 98.0 ··· 214433 s at SELENBP1 244409 at CCDC154 98.0 ··· 229541 at NA 244409 at CCDC154 98.0 ··· 229541 at NA 240911 at NOS1 98.0 ··· 229541 at NA 239132 at NOS1 98.0 ··· 204214 s at RAB32 233632 s at XRN1 98.0 ··· 204214 s at RAB32 244409 at CCDC154 98.0 ··· 228911 at ADAMTS7 244409 at CCDC154 98.0 ··· 201719 s at EPB41L2 233632 s at XRN1 98.0 ··· 201719 s at EPB41L2 244409 at CCDC154 98.0 ··· 222400 s at ADI1 233632 s at XRN1 98.0 ··· 222400 s at ADI1 244409 at CCDC154 98.0 ··· 204854 at LEPREL2 244409 at CCDC154 98.0 ··· 204854 at LEPREL2 240911 at NOS1 98.0 ··· 204854 at LEPREL2 239132 at NOS1 98.0 ··· 223165 s at IP6K2 244409 at CCDC154 98.0 ··· 228790 at FAM110B 244409 at CCDC154 98.0 ··· 206217 at EDA 244409 at CCDC154 98.0 ··· 220014 at PRR16 244409 at CCDC154 98.0 ··· 210674 s at NA 244409 at CCDC154 98.0 ··· 210674 s at NA 240911 at NOS1 98.0 ··· 210674 s at NA 231916 at NOS1 98.0 ··· 210674 s at NA 239132 at NOS1 98.0 ··· 203669 s at DGAT1 244409 at CCDC154 98.0 ··· 205031 at EFNB3 244409 at CCDC154 98.0 ··· 218826 at SLC35F2 233632 s at XRN1 98.0 ··· 218826 at SLC35F2 244409 at CCDC154 98.0 ··· 240494 at NA 244409 at CCDC154 98.0 ··· 240494 at NA 240911 at NOS1 98.0 ··· 240494 at NA 1556606 at 0V2 98.0 ··· 240494 at NA 221605 s at PIPOX 98.0 ··· 240494 at NA 231916 at NOS1 98.0 ··· 240494 at NA 239132 at NOS1 98.0 ··· 227300 at TMEM119 244409 at CCDC154 98.0 ··· 227300 at TMEM119 240911 at NOS1 98.0 ··· 212382 at TCF4 244409 at CCDC154 98.0 ··· 212192 at KCTD12 244409 at CCDC154 98.0 ··· 201030 x at LDHB 244409 at CCDC154 98.0 ··· 230920 at LOC388630 244409 at CCDC154 98.0 ··· 230920 at LOC388630 240911 at NOS1 98.0 ···

59 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 230920 at LOC388630 239132 at NOS1 98.0 ··· 217809 at BZW2 244409 at CCDC154 98.0 ··· 238612 at NA 244409 at CCDC154 98.0 ··· 238612 at NA 240911 at NOS1 98.0 ··· 221272 s at C1orf21 244409 at CCDC154 98.0 ··· 230183 at EXT1 244409 at CCDC154 98.0 ··· 232935 at NA 244409 at CCDC154 98.0 ··· 232935 at NA 240911 at NOS1 98.0 ··· 232935 at NA 221605 s at PIPOX 98.0 ··· 227628 at GPX8 244409 at CCDC154 98.0 ··· 227628 at GPX8 240911 at NOS1 98.0 ··· 205398 s at SMAD3 244409 at CCDC154 98.0 ··· 206746 at BFSP1 244409 at CCDC154 98.0 ··· 229819 at A1BG 244409 at CCDC154 98.0 ··· 229819 at A1BG 240911 at NOS1 98.0 ··· 219685 at TMEM35 244409 at CCDC154 98.0 ··· 202955 s at ARFGEF1 244409 at CCDC154 98.0 ··· 241729 at DOK6 214180 at MAN1C1 98.0 ··· 241729 at DOK6 244409 at CCDC154 98.0 ··· 241729 at DOK6 240911 at NOS1 98.0 ··· 241729 at DOK6 239132 at NOS1 98.0 ··· 219798 s at MEPCE 244409 at CCDC154 98.0 ··· 208711 s at CCND1 244409 at CCDC154 98.0 ··· 219215 s at SLC39A4 244409 at CCDC154 98.0 ··· 205020 s at ARL4A 244409 at CCDC154 98.0 ··· 212016 s at PTBP1 244409 at CCDC154 98.0 ··· 208843 s at GORASP2 244409 at CCDC154 98.0 ··· 222124 at HIF3A 244409 at CCDC154 98.0 ··· 226288 s at NLGN2 244409 at CCDC154 98.0 ··· 226288 s at NLGN2 240911 at NOS1 98.0 ··· 226949 at GOLGA3 244409 at CCDC154 98.0 ··· 221734 at PRRC1 244409 at CCDC154 98.0 ··· 218031 s at FOXN3 233632 s at XRN1 98.0 ··· 218031 s at FOXN3 244409 at CCDC154 98.0 ··· 202561 at TNKS 244409 at CCDC154 98.0 ··· 214394 x at EEF1D 244409 at CCDC154 98.0 ··· 225378 at VPS37A 244409 at CCDC154 98.0 ··· 225378 at VPS37A 240911 at NOS1 98.0 ··· 203449 s at TERF1 244409 at CCDC154 98.0 ··· 201367 s at ZFP36L2 233632 s at XRN1 98.0 ··· 201367 s at ZFP36L2 244409 at CCDC154 98.0 ··· 233834 at NA 244409 at CCDC154 98.0 ··· 233834 at NA 240911 at NOS1 98.0 ··· 233834 at NA 1556606 at 0V2 98.0 ··· 233834 at NA 239132 at NOS1 98.0 ··· 224020 at MGC4473 244409 at CCDC154 98.0 ··· 224020 at MGC4473 240911 at NOS1 98.0 ··· 224020 at MGC4473 1556606 at 0V2 98.0 ··· 224020 at MGC4473 239132 at NOS1 98.0 ··· 218656 s at LHFP 244409 at CCDC154 98.0 ··· 228949 at WLS 233632 s at XRN1 98.0 ··· 228949 at WLS 225814 at XRN1 98.0 ··· 228949 at WLS 244409 at CCDC154 98.0 ··· 228949 at WLS 240911 at NOS1 98.0 ··· 230412 at NPAS3 244409 at CCDC154 98.0 ··· 204040 at RNF144A 244409 at CCDC154 98.0 ··· 224413 s at TM2D2 244409 at CCDC154 98.0 ··· 224413 s at TM2D2 240911 at NOS1 98.0 ··· 224413 s at TM2D2 239132 at NOS1 98.0 ··· 212461 at AZIN1 244409 at CCDC154 98.0 ··· 213519 s at LAMA2 244409 at CCDC154 98.0 ··· 202722 s at GFPT1 244409 at CCDC154 98.0 ··· 225400 at TSEN15 244409 at CCDC154 98.0 ··· 225400 at TSEN15 240911 at NOS1 98.0 ··· 225400 at TSEN15 239132 at NOS1 98.0 ··· 225029 at LOC550643 244409 at CCDC154 98.0 ··· 225029 at LOC550643 240911 at NOS1 98.0 ··· 236219 at SLC35G1 244409 at CCDC154 98.0 ···

60 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 236219 at SLC35G1 240911 at NOS1 98.0 ··· 236219 at SLC35G1 1556606 at 0V2 98.0 ··· 236219 at SLC35G1 221605 s at PIPOX 98.0 ··· 236219 at SLC35G1 231916 at NOS1 98.0 ··· 236219 at SLC35G1 239132 at NOS1 98.0 ··· 222454 s at PARVA 233632 s at XRN1 98.0 ··· 222454 s at PARVA 244409 at CCDC154 98.0 ··· 219197 s at SCUBE2 244409 at CCDC154 98.0 ··· 202824 s at TCEB1 244409 at CCDC154 98.0 ··· 205696 s at GFRA1 244409 at CCDC154 98.0 ··· 201183 s at CHD4 244409 at CCDC154 98.0 ··· 213391 at DPY19L4 244409 at CCDC154 98.0 ··· 1558404 at LOC644242 244409 at CCDC154 98.0 ··· 1558404 at LOC644242 240911 at NOS1 98.0 ··· 206194 at NA 244409 at CCDC154 98.0 ··· 206194 at NA 240911 at NOS1 98.0 ··· 206194 at NA 239132 at NOS1 98.0 ··· 210419 at BARX2 244409 at CCDC154 98.0 ··· 1559840 s at TBX18 244409 at CCDC154 98.0 ··· 1559840 s at TBX18 240911 at NOS1 98.0 ··· 1559840 s at TBX18 1556606 at 0V2 98.0 ··· 1559840 s at TBX18 239132 at NOS1 98.0 ··· 225032 at FNDC3B 233632 s at XRN1 98.0 ··· 225032 at FNDC3B 225814 at XRN1 98.0 ··· 225032 at FNDC3B 244409 at CCDC154 98.0 ··· 1558507 at C1orf53 244409 at CCDC154 98.0 ··· 1558507 at C1orf53 240911 at NOS1 98.0 ··· 209282 at PRKD2 233632 s at XRN1 98.0 ··· 209282 at PRKD2 225814 at XRN1 98.0 ··· 209282 at PRKD2 244409 at CCDC154 98.0 ··· 216840 s at LAMA2 244409 at CCDC154 98.0 ··· 235758 at PNMA6C 244409 at CCDC154 98.0 ··· 235758 at PNMA6C 240911 at NOS1 98.0 ··· 235758 at PNMA6C 239132 at NOS1 98.0 ··· 202345 s at FABP5 244409 at CCDC154 98.0 ··· 218284 at SMAD3 233632 s at XRN1 98.0 ··· 218284 at SMAD3 225814 at XRN1 98.0 ··· 218284 at SMAD3 244409 at CCDC154 98.0 ··· 227263 at C8orf58 244409 at CCDC154 98.0 ··· 227263 at C8orf58 240911 at NOS1 98.0 ··· 227263 at C8orf58 214451 at TFAP2B 98.0 ··· 227263 at C8orf58 239132 at NOS1 98.0 ··· 200755 s at CALU 244409 at CCDC154 98.0 ··· 219312 s at ZBTB10 244409 at CCDC154 98.0 ··· 201605 x at CNN2 244409 at CCDC154 98.0 ··· 243903 at NA 244409 at CCDC154 98.0 ··· 243903 at NA 240911 at NOS1 98.0 ··· 243903 at NA 221605 s at PIPOX 98.0 ··· 243903 at NA 239132 at NOS1 98.0 ··· 218465 at TMEM33 244409 at CCDC154 98.0 ··· 200773 x at PTMA 244409 at CCDC154 98.0 ··· 207144 s at CITED1 244409 at CCDC154 98.0 ··· 228035 at STK33 244409 at CCDC154 98.0 ··· 228035 at STK33 240911 at NOS1 98.0 ··· 224397 s at TMTC1 244409 at CCDC154 98.0 ··· 224397 s at TMTC1 240911 at NOS1 98.0 ··· 224397 s at TMTC1 239132 at NOS1 98.0 ··· 206601 s at HOXD3 244409 at CCDC154 98.0 ··· 232201 at NKD2 244409 at CCDC154 98.0 ··· 232201 at NKD2 240911 at NOS1 98.0 ··· 206106 at NA 240911 at NOS1 98.0 ··· 235337 at SERTAD4 244409 at CCDC154 98.0 ··· 235337 at SERTAD4 240911 at NOS1 98.0 ··· 219922 s at LTBP3 225305 at SLC25A29 98.0 ··· 219922 s at LTBP3 244409 at CCDC154 98.0 ··· 219520 s at WWC3 233632 s at XRN1 98.0 ··· 219520 s at WWC3 225814 at XRN1 98.0 ··· 219520 s at WWC3 244409 at CCDC154 98.0 ···

61 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 202728 s at LTBP1 244409 at CCDC154 98.0 ··· 212377 s at NOTCH2 233632 s at XRN1 98.0 ··· 212377 s at NOTCH2 225814 at XRN1 98.0 ··· 212377 s at NOTCH2 244409 at CCDC154 98.0 ··· 202721 s at GFPT1 244409 at CCDC154 98.0 ··· 239907 at NA 233632 s at XRN1 98.0 ··· 239907 at NA 244409 at CCDC154 98.0 ··· 239907 at NA 240911 at NOS1 98.0 ··· 239907 at NA 239132 at NOS1 98.0 ··· 220967 s at ZNF696 244409 at CCDC154 98.0 ··· 204983 s at GPC4 244409 at CCDC154 98.0 ··· 202505 at SNRPB2 244409 at CCDC154 98.0 ··· 218454 at PLBD1 233632 s at XRN1 98.0 ··· 218454 at PLBD1 244409 at CCDC154 98.0 ··· 213150 at HOXA10 244409 at CCDC154 98.0 ··· 227195 at ZNF503 233632 s at XRN1 98.0 ··· 227195 at ZNF503 244409 at CCDC154 98.0 ··· 227195 at ZNF503 240911 at NOS1 98.0 ··· 227354 at PAG1 244409 at CCDC154 98.0 ··· 227354 at PAG1 240911 at NOS1 98.0 ··· 233003 at NA 233632 s at XRN1 98.0 ··· 233003 at NA 244409 at CCDC154 98.0 ··· 233003 at NA 240911 at NOS1 98.0 ··· 233003 at NA 239132 at NOS1 98.0 ··· 230456 at NA 244409 at CCDC154 98.0 ··· 230456 at NA 240911 at NOS1 98.0 ··· 235775 at TMTC2 207077 at CELA2B 98.0 ··· 235775 at TMTC2 225814 at XRN1 98.0 ··· 235775 at TMTC2 244409 at CCDC154 98.0 ··· 235775 at TMTC2 240911 at NOS1 98.0 ··· 200700 s at KDELR2 244409 at CCDC154 98.0 ··· 226698 at FCHSD1 244409 at CCDC154 98.0 ··· 226698 at FCHSD1 240911 at NOS1 98.0 ··· 210829 s at SSBP2 244409 at CCDC154 98.0 ··· 203261 at DCTN6 244409 at CCDC154 98.0 ··· 235891 at MIR214 244409 at CCDC154 98.0 ··· 235891 at MIR214 240911 at NOS1 98.0 ··· 235891 at MIR214 221605 s at PIPOX 98.0 ··· 244217 at NA 244409 at CCDC154 98.0 ··· 244217 at NA 240911 at NOS1 98.0 ··· 218172 s at DERL1 244409 at CCDC154 98.0 ··· 200990 at TRIM28 244409 at CCDC154 98.0 ··· 223468 s at RGMA 244409 at CCDC154 98.0 ··· 223468 s at RGMA 240911 at NOS1 98.0 ··· 1555707 at T0P 206446 s at NA 98.0 ··· 1555707 at T0P 244409 at CCDC154 98.0 ··· 1555707 at T0P 240911 at NOS1 98.0 ··· 1555707 at T0P 221605 s at PIPOX 98.0 ··· 1555707 at T0P 231916 at NOS1 98.0 ··· 1555707 at T0P 239132 at NOS1 98.0 ··· 202710 at BET1 244409 at CCDC154 98.0 ··· 209218 at SQLE 223974 at MGC11082 98.0 ··· 209218 at SQLE 244409 at CCDC154 98.0 ··· 225857 s at LOC388796 244409 at CCDC154 98.0 ··· 212096 s at MTUS1 233632 s at XRN1 98.0 ··· 212096 s at MTUS1 225814 at XRN1 98.0 ··· 212096 s at MTUS1 244409 at CCDC154 98.0 ··· 203207 s at MTFR1 244409 at CCDC154 98.0 ··· 212724 at RND3 244409 at CCDC154 98.0 ··· 209817 at PPP3CB 244409 at CCDC154 98.0 ··· 231130 at FKBP7 244409 at CCDC154 98.0 ··· 231130 at FKBP7 240911 at NOS1 98.0 ··· 231130 at FKBP7 239132 at NOS1 98.0 ··· 227727 at MRGPRF 225814 at XRN1 98.0 ··· 227727 at MRGPRF 244409 at CCDC154 98.0 ··· 227727 at MRGPRF 240911 at NOS1 98.0 ··· 225979 at PLEKHG2 244409 at CCDC154 98.0 ··· 225979 at PLEKHG2 1556606 at 0V2 98.0 ···

62 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 225979 at PLEKHG2 221605 s at PIPOX 98.0 ··· 227083 at B3GALTL 244409 at CCDC154 98.0 ··· 227083 at B3GALTL 240911 at NOS1 98.0 ··· 227083 at B3GALTL 1556606 at 0V2 98.0 ··· 227083 at B3GALTL 231916 at NOS1 98.0 ··· 222694 at MGC2752 244409 at CCDC154 98.0 ··· 201069 at MMP2 244409 at CCDC154 98.0 ··· 200051 at SART1 244409 at CCDC154 98.0 ··· 222494 at FOXN3 233632 s at XRN1 98.0 ··· 222494 at FOXN3 225814 at XRN1 98.0 ··· 222494 at FOXN3 244409 at CCDC154 98.0 ··· 232983 s at SERGEF 244409 at CCDC154 98.0 ··· 235106 at MAML2 233632 s at XRN1 98.0 ··· 235106 at MAML2 244409 at CCDC154 98.0 ··· 235106 at MAML2 240911 at NOS1 98.0 ··· 207030 s at CSRP2 244409 at CCDC154 98.0 ··· 205022 s at FOXN3 233632 s at XRN1 98.0 ··· 205022 s at FOXN3 225814 at XRN1 98.0 ··· 205022 s at FOXN3 244409 at CCDC154 98.0 ··· 221922 at GPSM2 244409 at CCDC154 98.0 ··· 223378 at GLIS2 244409 at CCDC154 98.0 ··· 223378 at GLIS2 240911 at NOS1 98.0 ··· 221770 at RPE 238432 at FLJ35776 98.0 ··· 221770 at RPE 244409 at CCDC154 98.0 ··· 212166 at XPO7 244409 at CCDC154 98.0 ··· 225308 s at TANC1 233632 s at XRN1 98.0 ··· 225308 s at TANC1 244409 at CCDC154 98.0 ··· 225308 s at TANC1 240911 at NOS1 98.0 ··· 225308 s at TANC1 230076 at PITPNM3 98.0 ··· 225308 s at TANC1 1556606 at 0V2 98.0 ··· 225308 s at TANC1 221605 s at PIPOX 98.0 ··· 225308 s at TANC1 239132 at NOS1 98.0 ··· 202788 at MAPKAPK3 244409 at CCDC154 98.0 ··· 200623 s at CALM3 244409 at CCDC154 98.0 ··· 225406 at TWSG1 244409 at CCDC154 98.0 ··· 201287 s at SDC1 244409 at CCDC154 98.0 ··· 213113 s at SLC43A3 244409 at CCDC154 98.0 ··· 221123 x at ZNF395 244409 at CCDC154 98.0 ··· 209808 x at ING1 244409 at CCDC154 98.0 ··· 204301 at KBTBD11 244409 at CCDC154 98.0 ··· 219060 at WDYHV1 244409 at CCDC154 98.0 ··· 235117 at CHAC2 244409 at CCDC154 98.0 ··· 235117 at CHAC2 240911 at NOS1 98.0 ··· 228228 at DACT3 244409 at CCDC154 98.0 ··· 228228 at DACT3 240911 at NOS1 98.0 ··· 201512 s at TOMM70A 244409 at CCDC154 98.0 ··· 214003 x at RPS20 244409 at CCDC154 98.0 ··· 220316 at NPAS3 244409 at CCDC154 98.0 ··· 220134 x at FAM176B 244409 at CCDC154 98.0 ··· 202218 s at FADS2 244409 at CCDC154 98.0 ··· 227765 at LOC100506365 244409 at CCDC154 98.0 ··· 227765 at LOC100506365 240911 at NOS1 98.0 ··· 227765 at LOC100506365 1556606 at 0V2 98.0 ··· 205397 x at SMAD3 244409 at CCDC154 98.0 ··· 218900 at CNNM4 244409 at CCDC154 98.0 ··· 201281 at ADRM1 244409 at CCDC154 98.0 ··· 221253 s at NA 244409 at CCDC154 98.0 ··· 221253 s at NA 240911 at NOS1 98.0 ··· 218125 s at CCDC25 244409 at CCDC154 98.0 ··· 212413 at 6-Sep 244409 at CCDC154 98.0 ··· 226331 at BBX 206447 at NA 98.0 ··· 226331 at BBX 225814 at XRN1 98.0 ··· 226331 at BBX 244409 at CCDC154 98.0 ··· 202174 s at PCM1 244409 at CCDC154 98.0 ··· 227328 at CAMTA1 244409 at CCDC154 98.0 ··· 58780 s at ARHGEF40 225814 at XRN1 98.0 ··· 58780 s at ARHGEF40 244409 at CCDC154 98.0 ··· 58780 s at ARHGEF40 240911 at NOS1 98.0 ···

63 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 209983 s at NRXN2 244409 at CCDC154 98.0 ··· 222986 s at SHISA5 244409 at CCDC154 98.0 ··· 222986 s at SHISA5 240911 at NOS1 98.0 ··· 1555037 a at IDH1 244409 at CCDC154 98.0 ··· 228253 at LOXL3 244409 at CCDC154 98.0 ··· 228253 at LOXL3 240911 at NOS1 98.0 ··· 231034 s at NHSL1 244409 at CCDC154 98.0 ··· 231034 s at NHSL1 240911 at NOS1 98.0 ··· 231034 s at NHSL1 221605 s at PIPOX 98.0 ··· 231034 s at NHSL1 239132 at NOS1 98.0 ··· 209418 s at THOC5 244409 at CCDC154 98.0 ··· 201193 at IDH1 244409 at CCDC154 98.0 ··· 227376 at GLI3 244409 at CCDC154 98.0 ··· 208704 x at APLP2 244409 at CCDC154 98.0 ··· 203113 s at EEF1D 244409 at CCDC154 98.0 ··· 212484 at FAM89B 244409 at CCDC154 98.0 ··· 221579 s at NUDT3 244409 at CCDC154 98.0 ··· 218955 at BRF2 244409 at CCDC154 98.0 ··· 214649 s at MTMR2 244409 at CCDC154 98.0 ··· 215084 s at LRRC42 244409 at CCDC154 98.0 ··· 202815 s at HEXIM1 244409 at CCDC154 98.0 ··· 205990 s at WNT5A 244409 at CCDC154 98.0 ··· 200949 x at RPS20 244409 at CCDC154 98.0 ··· 219201 s at TWSG1 244409 at CCDC154 98.0 ··· 200640 at YWHAZ 244409 at CCDC154 98.0 ··· 229278 at USP51 244409 at CCDC154 98.0 ··· 229278 at USP51 240911 at NOS1 98.0 ··· 229278 at USP51 239132 at NOS1 98.0 ··· 215672 s at AHCYL2 244409 at CCDC154 98.0 ··· 229016 s at TRERF1 244409 at CCDC154 98.0 ··· 229016 s at TRERF1 240911 at NOS1 98.0 ··· 204679 at KCNK1 244409 at CCDC154 98.0 ··· 46665 at SEMA4C 244409 at CCDC154 98.0 ··· 232174 at NA 244409 at CCDC154 98.0 ··· 232174 at NA 240911 at NOS1 98.0 ··· 232174 at NA 1556606 at 0V2 98.0 ··· 232174 at NA 239132 at NOS1 98.0 ··· 1554155 at MCPH1 244409 at CCDC154 98.0 ··· 205770 at GSR 244409 at CCDC154 98.0 ··· 239220 at NA 244409 at CCDC154 98.0 ··· 239220 at NA 240911 at NOS1 98.0 ··· 221629 x at FAM203A 244409 at CCDC154 98.0 ··· 221629 x at FAM203A 240911 at NOS1 98.0 ··· 221629 x at FAM203A 1556606 at 0V2 98.0 ··· 221629 x at FAM203A 239132 at NOS1 98.0 ··· 221781 s at D0JC10 244409 at CCDC154 98.0 ··· 222657 s at UBE2W 244409 at CCDC154 98.0 ··· 212823 s at PLEKHG3 244409 at CCDC154 98.0 ··· 208702 x at APLP2 244409 at CCDC154 98.0 ··· 223595 at TMEM133 233632 s at XRN1 98.0 ··· 223595 at TMEM133 225814 at XRN1 98.0 ··· 223595 at TMEM133 244409 at CCDC154 98.0 ··· 223595 at TMEM133 240911 at NOS1 98.0 ··· 223595 at TMEM133 221605 s at PIPOX 98.0 ··· 223595 at TMEM133 239132 at NOS1 98.0 ··· 201983 s at EGFR 225814 at XRN1 98.0 ··· 201983 s at EGFR 244409 at CCDC154 98.0 ··· 209675 s at HNRNPUL1 244409 at CCDC154 98.0 ··· 238447 at RBMS3 244409 at CCDC154 98.0 ··· 1556429 a at WDR67 244409 at CCDC154 98.0 ··· 218425 at RNF216 244409 at CCDC154 98.0 ··· 226109 at C21orf91 233632 s at XRN1 98.0 ··· 226109 at C21orf91 225814 at XRN1 98.0 ··· 226109 at C21orf91 244409 at CCDC154 98.0 ··· 234610 at HSPA12B 244409 at CCDC154 98.0 ··· 234610 at HSPA12B 240911 at NOS1 98.0 ··· 203451 at LDB1 244409 at CCDC154 98.0 ··· 35160 at LDB1 244409 at CCDC154 98.0 ···

64 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 225303 at KIRREL 244409 at CCDC154 98.0 ··· 202635 s at POLR2K 244409 at CCDC154 98.0 ··· 1569024 at FAM13A 244409 at CCDC154 98.0 ··· 1552422 at C10orf25 244409 at CCDC154 98.0 ··· 1552422 at C10orf25 240911 at NOS1 98.0 ··· 1552422 at C10orf25 1556606 at 0V2 98.0 ··· 1552422 at C10orf25 239132 at NOS1 98.0 ··· 218516 s at IMPAD1 244409 at CCDC154 98.0 ··· 230480 at PIWIL4 244409 at CCDC154 98.0 ··· 230480 at PIWIL4 240911 at NOS1 98.0 ··· 230480 at PIWIL4 239132 at NOS1 98.0 ··· 221652 s at ASUN 244409 at CCDC154 98.0 ··· 221652 s at ASUN 240911 at NOS1 98.0 ··· 200922 at KDELR1 244409 at CCDC154 98.0 ··· 206373 at ZIC1 244409 at CCDC154 98.0 ··· 204068 at STK3 233632 s at XRN1 98.0 ··· 204068 at STK3 225814 at XRN1 98.0 ··· 204068 at STK3 244409 at CCDC154 98.0 ··· 202946 s at BTBD3 233632 s at XRN1 98.0 ··· 202946 s at BTBD3 244409 at CCDC154 98.0 ··· 225871 at STEAP2 244409 at CCDC154 98.0 ··· 225871 at STEAP2 240911 at NOS1 98.0 ··· 216266 s at ARFGEF1 244409 at CCDC154 98.0 ··· 231767 at HOXB4 244409 at CCDC154 98.0 ··· 231767 at HOXB4 240911 at NOS1 98.0 ··· 218932 at ZNHIT6 244409 at CCDC154 98.0 ··· 1557331 at POLR1B 206446 s at NA 98.0 ··· 1557331 at POLR1B 244409 at CCDC154 98.0 ··· 207011 s at PTK7 244409 at CCDC154 98.0 ··· 200717 x at RPL7 244409 at CCDC154 98.0 ··· 219973 at ARSJ 233632 s at XRN1 98.0 ··· 219973 at ARSJ 244409 at CCDC154 98.0 ··· 239942 at NA 244409 at CCDC154 98.0 ··· 239942 at NA 240911 at NOS1 98.0 ··· 1554063 at NA 233632 s at XRN1 98.0 ··· 1554063 at NA 225814 at XRN1 98.0 ··· 1554063 at NA 244409 at CCDC154 98.0 ··· 1554063 at NA 240911 at NOS1 98.0 ··· 1554063 at NA 1556606 at 0V2 98.0 ··· 1554063 at NA 221605 s at PIPOX 98.0 ··· 1554063 at NA 239132 at NOS1 98.0 ··· 214875 x at APLP2 244409 at CCDC154 98.0 ··· 210137 s at DCTD 233632 s at XRN1 98.0 ··· 210137 s at DCTD 244409 at CCDC154 98.0 ··· 226463 at ATP6V1C1 244409 at CCDC154 98.0 ··· 1554586 a at RHOBTB2 244409 at CCDC154 98.0 ··· 216176 at HCRP1 244409 at CCDC154 98.0 ··· 1559822 s at MTDH 244409 at CCDC154 98.0 ··· 226386 at MALSU1 244409 at CCDC154 98.0 ··· 226386 at MALSU1 240911 at NOS1 98.0 ··· 225169 at INTS4 244409 at CCDC154 98.0 ··· 225169 at INTS4 240911 at NOS1 98.0 ··· 225169 at INTS4 230076 at PITPNM3 98.0 ··· 225169 at INTS4 1556606 at 0V2 98.0 ··· 225169 at INTS4 231916 at NOS1 98.0 ··· 225169 at INTS4 239132 at NOS1 98.0 ··· 202443 x at NOTCH2 233632 s at XRN1 98.0 ··· 202443 x at NOTCH2 225814 at XRN1 98.0 ··· 202443 x at NOTCH2 244409 at CCDC154 98.0 ··· 209544 at RIPK2 244409 at CCDC154 98.0 ··· 207668 x at PDIA6 244409 at CCDC154 98.0 ··· 214626 s at GA0B 244409 at CCDC154 98.0 ··· 1559965 at LOC100192378 244409 at CCDC154 98.0 ··· 1559965 at LOC100192378 240911 at NOS1 98.0 ··· 202431 s at MYC 244409 at CCDC154 98.0 ··· 225464 at FRMD6 233632 s at XRN1 98.0 ··· 225464 at FRMD6 244409 at CCDC154 98.0 ··· 225464 at FRMD6 240911 at NOS1 98.0 ···

65 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 209708 at MOXD1 244409 at CCDC154 98.0 ··· 228555 at CAMK2D 244409 at CCDC154 98.0 ··· 228555 at CAMK2D 240911 at NOS1 98.0 ··· 214797 s at CDK18 244409 at CCDC154 98.0 ··· 219126 at PHF10 244409 at CCDC154 98.0 ··· 233044 at NA 244409 at CCDC154 98.0 ··· 233044 at NA 240911 at NOS1 98.0 ··· 220474 at SLC25A21 244409 at CCDC154 98.0 ··· 225544 at TBX3 244409 at CCDC154 98.0 ··· 232927 at NA 233632 s at XRN1 98.0 ··· 232927 at NA 244409 at CCDC154 98.0 ··· 232927 at NA 240911 at NOS1 98.0 ··· 232927 at NA 1556606 at 0V2 98.0 ··· 232927 at NA 221605 s at PIPOX 98.0 ··· 232927 at NA 231916 at NOS1 98.0 ··· 232927 at NA 239132 at NOS1 98.0 ··· 208523 x at HIST1H2BI 244409 at CCDC154 98.0 ··· 220382 s at ARHGAP28 244409 at CCDC154 98.0 ··· 210762 s at DLC1 244409 at CCDC154 98.0 ··· 201571 s at DCTD 244409 at CCDC154 98.0 ··· 200756 x at CALU 244409 at CCDC154 98.0 ··· 228810 at CCNYL1 244409 at CCDC154 98.0 ··· 228810 at CCNYL1 240911 at NOS1 98.0 ··· 241386 at LOC100506691 244409 at CCDC154 98.0 ··· 241386 at LOC100506691 240911 at NOS1 98.0 ··· 218162 at OLFML3 244409 at CCDC154 98.0 ··· 237031 at NA 244409 at CCDC154 98.0 ··· 237031 at NA 240911 at NOS1 98.0 ··· 237031 at NA 1556606 at 0V2 98.0 ··· 216836 s at ERBB2 244409 at CCDC154 98.0 ··· 222654 at IMPAD1 238432 at FLJ35776 98.0 ··· 222654 at IMPAD1 244409 at CCDC154 98.0 ··· 227411 at WTIP 244409 at CCDC154 98.0 ··· 227411 at WTIP 221605 s at PIPOX 98.0 ··· 230047 at ARHGAP42 233632 s at XRN1 98.0 ··· 230047 at ARHGAP42 225814 at XRN1 98.0 ··· 230047 at ARHGAP42 244409 at CCDC154 98.0 ··· 230047 at ARHGAP42 240911 at NOS1 98.0 ··· 230047 at ARHGAP42 221605 s at PIPOX 98.0 ··· 230047 at ARHGAP42 231916 at NOS1 98.0 ··· 230047 at ARHGAP42 239132 at NOS1 98.0 ··· 208476 s at FRMD4A 244409 at CCDC154 98.0 ··· 221786 at C6orf120 1553394 a at TFAP2B 98.0 ··· 221786 at C6orf120 244409 at CCDC154 98.0 ··· 220147 s at FAM60A 244409 at CCDC154 98.0 ··· 210756 s at NOTCH2 233632 s at XRN1 98.0 ··· 210756 s at NOTCH2 244409 at CCDC154 98.0 ··· 201286 at SDC1 244409 at CCDC154 98.0 ··· 219904 at ZSCAN5A 244409 at CCDC154 98.0 ··· 210257 x at CUL4B 244409 at CCDC154 98.0 ··· 226490 at NHSL1 244409 at CCDC154 98.0 ··· 226490 at NHSL1 240911 at NOS1 98.0 ··· 226490 at NHSL1 221605 s at PIPOX 98.0 ··· 226490 at NHSL1 239132 at NOS1 98.0 ··· 218926 at MYNN 244409 at CCDC154 98.0 ··· 1566551 at NA 244409 at CCDC154 98.0 ··· 1566551 at NA 240911 at NOS1 98.0 ··· 1566551 at NA 239132 at NOS1 98.0 ··· 229674 at SERTAD4 244409 at CCDC154 98.0 ··· 229674 at SERTAD4 240911 at NOS1 98.0 ··· 215983 s at UBXN8 244409 at CCDC154 98.0 ··· 223024 at AP1M1 244409 at CCDC154 98.0 ··· 223024 at AP1M1 240911 at NOS1 98.0 ··· 202595 s at LEPROTL1 244409 at CCDC154 98.0 ··· 209893 s at FUT4 244409 at CCDC154 98.0 ··· 224675 at MESDC2 244409 at CCDC154 98.0 ··· 224675 at MESDC2 240911 at NOS1 98.0 ··· 229296 at NA 244409 at CCDC154 98.0 ···

66 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 229296 at NA 240911 at NOS1 98.0 ··· 232012 at CAPN1 233632 s at XRN1 98.0 ··· 232012 at CAPN1 244409 at CCDC154 98.0 ··· 202212 at PES1 244409 at CCDC154 98.0 ··· 215418 at PARVA 233632 s at XRN1 98.0 ··· 215418 at PARVA 225814 at XRN1 98.0 ··· 215418 at PARVA 244409 at CCDC154 98.0 ··· 203114 at SSSCA1 244409 at CCDC154 98.0 ··· 203431 s at ARHGAP32 244409 at CCDC154 98.0 ··· 227557 at SCARF2 244409 at CCDC154 98.0 ··· 227557 at SCARF2 240911 at NOS1 98.0 ··· 236656 s at LOC100288911 244409 at CCDC154 98.0 ··· 236656 s at LOC100288911 240911 at NOS1 98.0 ··· 200639 s at YWHAZ 244409 at CCDC154 98.0 ··· 233917 s at MOV10 225305 at SLC25A29 98.0 ··· 233917 s at MOV10 244409 at CCDC154 98.0 ··· 231823 s at SH3PXD2B 244409 at CCDC154 98.0 ··· 231823 s at SH3PXD2B 240911 at NOS1 98.0 ··· 223614 at MMP16 244409 at CCDC154 98.0 ··· 223591 at RNF135 244409 at CCDC154 98.0 ··· 223591 at RNF135 240911 at NOS1 98.0 ··· 201754 at COX6C 244409 at CCDC154 98.0 ··· 238561 s at UTP23 244409 at CCDC154 98.0 ··· 238561 s at UTP23 240911 at NOS1 98.0 ··· 209428 s at ZFPL1 244409 at CCDC154 98.0 ··· 221586 s at E2F5 244409 at CCDC154 98.0 ··· 221923 s at NPM1 244409 at CCDC154 98.0 ··· 91952 at DCAF15 244409 at CCDC154 98.0 ··· 218612 s at TSSC4 244409 at CCDC154 98.0 ··· 221767 x at HDLBP 244409 at CCDC154 98.0 ··· 223849 s at MOV10 244409 at CCDC154 98.0 ··· 243424 at NA 244409 at CCDC154 98.0 ··· 243424 at NA 240911 at NOS1 98.0 ··· 243424 at NA 221605 s at PIPOX 98.0 ··· 243424 at NA 239132 at NOS1 98.0 ··· 212466 at SPRED2 233632 s at XRN1 98.0 ··· 212466 at SPRED2 244409 at CCDC154 98.0 ··· 223095 at MARVELD1 244409 at CCDC154 98.0 ··· 223095 at MARVELD1 240911 at NOS1 98.0 ··· 223095 at MARVELD1 1556606 at 0V2 98.0 ··· 238436 s at ZNF805 244409 at CCDC154 98.0 ··· 238436 s at ZNF805 240911 at NOS1 98.0 ··· 200969 at SERP1 244409 at CCDC154 98.0 ··· 223306 at EBPL 244409 at CCDC154 98.0 ··· 223306 at EBPL 240911 at NOS1 98.0 ··· 223306 at EBPL 239132 at NOS1 98.0 ··· 1555618 s at SAE1 244409 at CCDC154 98.0 ··· 210791 s at ARHGAP32 244409 at CCDC154 98.0 ··· 219427 at FAT4 244409 at CCDC154 98.0 ··· 201592 at EIF3H 244409 at CCDC154 98.0 ··· 217784 at YKT6 244409 at CCDC154 98.0 ··· 212369 at ZNF384 244409 at CCDC154 98.0 ··· 210811 s at DDX49 244409 at CCDC154 98.0 ··· 228013 at PPP2R2A 244409 at CCDC154 98.0 ··· 228013 at PPP2R2A 221605 s at PIPOX 98.0 ··· 208248 x at APLP2 244409 at CCDC154 98.0 ··· 202956 at ARFGEF1 244409 at CCDC154 98.0 ··· 235046 at INPP4B 225814 at XRN1 98.0 ··· 235046 at INPP4B 244409 at CCDC154 98.0 ··· 235046 at INPP4B 221605 s at PIPOX 98.0 ··· 91684 g at EXOSC4 244409 at CCDC154 98.0 ··· 222714 s at LACTB2 244409 at CCDC154 98.0 ··· 218954 s at BRF2 244409 at CCDC154 98.0 ··· 209509 s at DPAGT1 244409 at CCDC154 98.0 ··· 201874 at MPZL1 244409 at CCDC154 98.0 ··· 1554153 a at PHF21A 244409 at CCDC154 98.0 ··· 1562234 a at 0V3 244409 at CCDC154 98.0 ··· 216466 at 0V3 244409 at CCDC154 98.0 ···

67 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 1557685 at LOC100507117 244409 at CCDC154 98.0 ··· 1557685 at LOC100507117 240911 at NOS1 98.0 ··· 1557685 at LOC100507117 221605 s at PIPOX 98.0 ··· 1557685 at LOC100507117 239132 at NOS1 98.0 ··· 211934 x at GA0B 244409 at CCDC154 98.0 ··· 225748 at LTV1 244409 at CCDC154 98.0 ··· 225748 at LTV1 240911 at NOS1 98.0 ··· 201937 s at DNPEP 244409 at CCDC154 98.0 ··· 212183 at NUDT4 244409 at CCDC154 98.0 ··· 218833 at ZAK 244409 at CCDC154 98.0 ··· 223211 at HACL1 244409 at CCDC154 98.0 ··· 223211 at HACL1 240911 at NOS1 98.0 ··· 211802 x at CAC01G 244409 at CCDC154 98.0 ··· 236290 at DOK6 244409 at CCDC154 98.0 ··· 236290 at DOK6 240911 at NOS1 98.0 ··· 204392 at CAMK1 244409 at CCDC154 98.0 ··· 205113 at NEFM 244409 at CCDC154 98.0 ··· 216397 s at BOP1 244409 at CCDC154 98.0 ··· 216397 s at BOP1 240911 at NOS1 98.0 ··· 224822 at DLC1 244409 at CCDC154 98.0 ··· 235362 at LOC729970 244409 at CCDC154 98.0 ··· 235362 at LOC729970 240911 at NOS1 98.0 ··· 235362 at LOC729970 239132 at NOS1 98.0 ··· 216680 s at EPHB4 244409 at CCDC154 98.0 ··· 201783 s at RELA 244409 at CCDC154 98.0 ··· 212098 at MGAT5 244409 at CCDC154 98.0 ··· 235311 at FKBP14 244409 at CCDC154 98.0 ··· 200599 s at HSP90B1 244409 at CCDC154 98.0 ··· 230660 at SERTAD4 244409 at CCDC154 98.0 ··· 230660 at SERTAD4 240911 at NOS1 98.0 ··· 203211 s at MTMR2 244409 at CCDC154 98.0 ··· 208883 at UBR5 244409 at CCDC154 98.0 ··· 216174 at HCRP1 244409 at CCDC154 98.0 ··· 203910 at ARHGAP29 233632 s at XRN1 98.0 ··· 203910 at ARHGAP29 225814 at XRN1 98.0 ··· 203910 at ARHGAP29 244409 at CCDC154 98.0 ··· 234974 at GALM 244409 at CCDC154 98.0 ··· 234974 at GALM 240911 at NOS1 98.0 ··· 213072 at CYHR1 244409 at CCDC154 98.0 ··· 218904 s at C9orf40 244409 at CCDC154 98.0 ··· 217996 at PHLDA1 244409 at CCDC154 98.0 ··· 225534 at C8orf40 244409 at CCDC154 98.0 ··· 225534 at C8orf40 240911 at NOS1 98.0 ··· 225534 at C8orf40 221605 s at PIPOX 98.0 ··· 225534 at C8orf40 239132 at NOS1 98.0 ··· 205407 at RECK 244409 at CCDC154 98.0 ··· 220470 at BET1L 244409 at CCDC154 98.0 ··· 209953 s at CDC37 244409 at CCDC154 98.0 ··· 207266 x at RBMS1 233632 s at XRN1 98.0 ··· 207266 x at RBMS1 244409 at CCDC154 98.0 ··· 211973 at NA 244409 at CCDC154 98.0 ··· 211973 at NA 240911 at NOS1 98.0 ··· 217047 s at FAM13A 225814 at XRN1 98.0 ··· 217047 s at FAM13A 244409 at CCDC154 98.0 ··· 214463 x at NA 244409 at CCDC154 98.0 ··· 214463 x at NA 240911 at NOS1 98.0 ··· 213045 at MAST3 244409 at CCDC154 98.0 ··· 1563635 at NA 244409 at CCDC154 98.0 ··· 1563635 at NA 240911 at NOS1 98.0 ··· 1563635 at NA 1556606 at 0V2 98.0 ··· 1563635 at NA 221605 s at PIPOX 98.0 ··· 1563635 at NA 239132 at NOS1 98.0 ··· 1559861 at NA 244409 at CCDC154 98.0 ··· 1559861 at NA 240911 at NOS1 98.0 ··· 1559861 at NA 1556606 at 0V2 98.0 ··· 211029 x at FGF18 244409 at CCDC154 98.0 ··· 235017 s at CSRNP3 244409 at CCDC154 98.0 ··· 230302 at NA 244409 at CCDC154 98.0 ···

68 SUPPLEMENTARY TABLE 2 — Continued

Probe Symbol Probe Symbol Classiﬁcation *Classiﬁcation Williamson Davicioni 230302 at NA 240911 at NOS1 98.0 ··· 230302 at NA 221605 s at PIPOX 98.0 ··· 230302 at NA 231916 at NOS1 98.0 ··· 230302 at NA 239132 at NOS1 98.0 ··· 200608 s at RAD21 244409 at CCDC154 98.0 ··· 221234 s at BACH2 244409 at CCDC154 98.0 ··· 224076 s at WHSC1L1 244409 at CCDC154 98.0 ··· 208700 s at TKT 244409 at CCDC154 98.0 ··· 209227 at TUSC3 244409 at CCDC154 98.0 ··· 215259 s at CADM4 244409 at CCDC154 98.0 ··· 225436 at FAM108C1 244409 at CCDC154 98.0 ··· 225436 at FAM108C1 240911 at NOS1 98.0 ··· 232148 at NSMAF 244409 at CCDC154 98.0 ··· 232148 at NSMAF 221605 s at PIPOX 98.0 ··· 219657 s at KLF3 244409 at CCDC154 98.0 ··· 202447 at DECR1 225814 at XRN1 98.0 ··· 202447 at DECR1 244409 at CCDC154 98.0 ··· 217092 x at RPL7 244409 at CCDC154 98.0 ··· 223452 s at ATL3 244409 at CCDC154 98.0 ··· 223452 s at ATL3 240911 at NOS1 98.0 ··· 235801 at TUSC3 244409 at CCDC154 98.0 ··· 235801 at TUSC3 221605 s at PIPOX 98.0 ··· 226575 at ZNF462 244409 at CCDC154 98.0 ··· 226575 at ZNF462 240911 at NOS1 98.0 ··· 207524 at ST7 244409 at CCDC154 98.0 ··· 204897 at PTGER4 233632 s at XRN1 98.0 ··· 204897 at PTGER4 225814 at XRN1 98.0 ··· 204897 at PTGER4 244409 at CCDC154 98.0 ··· 1554500 a at RGS7 244409 at CCDC154 98.0 ··· 225360 at TRABD 244409 at CCDC154 98.0 ··· 212611 at DTX4 244409 at CCDC154 98.0 ··· 208414 s at HOXB3 244409 at CCDC154 98.0 ··· 212481 s at TPM4 244409 at CCDC154 98.0 ··· 202440 s at ST5 233632 s at XRN1 98.0 ··· 202440 s at ST5 244409 at CCDC154 98.0 ··· 230728 at FKBP14 225814 at XRN1 98.0 ··· 230728 at FKBP14 244409 at CCDC154 98.0 ··· 205542 at STEAP1 244409 at CCDC154 98.0 ··· 220984 s at SLCO5A1 244409 at CCDC154 98.0 ··· 225267 at KP04 244409 at CCDC154 98.0 ··· 208580 x at NA 244409 at CCDC154 98.0 ··· 208580 x at NA 240911 at NOS1 98.0 ··· 226886 at GFPT1 244409 at CCDC154 98.0 ··· 212194 s at TM9SF4 244409 at CCDC154 98.0 ··· 219997 s at COPS7B 244409 at CCDC154 98.0 ··· 214512 s at SUB1 244409 at CCDC154 98.0 ··· 214937 x at PCM1 223974 at MGC11082 98.0 ··· 214937 x at PCM1 244409 at CCDC154 98.0 ··· 207069 s at SMAD6 233632 s at XRN1 98.0 ··· 207069 s at SMAD6 244409 at CCDC154 98.0 ··· 225313 at FAM217B 244409 at CCDC154 98.0 ··· 225313 at FAM217B 240911 at NOS1 98.0 ··· 225313 at FAM217B 230076 at PITPNM3 98.0 ··· 209385 s at PROSC 233632 s at XRN1 98.0 ··· 209385 s at PROSC 244409 at CCDC154 98.0 ··· 202033 s at RB1CC1 244409 at CCDC154 98.0 ··· 225481 at FRMD6 233632 s at XRN1 98.0 ··· 225481 at FRMD6 244409 at CCDC154 98.0 ··· 225481 at FRMD6 240911 at NOS1 98.0 ··· 225481 at FRMD6 214451 at TFAP2B 98.0 ··· 208989 s at KDM2A 244409 at CCDC154 98.0 ··· 202729 s at LTBP1 244409 at CCDC154 98.0 ··· 201380 at CRTAP 244409 at CCDC154 98.0 ··· 226559 at IER5L 244409 at CCDC154 98.0 ··· 226559 at IER5L 240911 at NOS1 98.0 ··· 214845 s at CALU 244409 at CCDC154 98.0 ···

69 SUPPLEMENTARY TABLE 3 T-test dyad classifier genes found in F1/F2 metagenes (L) and F1/F2 metagene probes excluded from dyad pairs (R)

Present F1/F2 metagenes Excluded from t-test pairs ARHGEF40 ABCG1 ASAP1 ALK ASS1 CAD CNR1 DAPK1 CPSF1 FAN1 EIF4EBP1 JARID2 FBN2 KCND3 FZD7 MAGI1 GALNT2 NELL1 GPX7 NRCAM HMGA2 NRN1 HOXC6 PGBD5 KAZN PTBP2 LAPTM4B RAP1GAP2 RBM13/MAK16 TAGLN3 MFAP2 TOX3 COLA2A/2B TULP4 PAFAH1B3 PGRMC1 PIPOX PSD3 SAE1 SOBP SPRED2 TFAP2B TRPS1 WDYHV1 WSCD1 ZIC1

70 SUPPLEMENTARY TABLE 4 Top-scoring classifiers from exhaustive search of 1.5 billion gene pairs *If no classification listed, probe/gene values were not available. Italics: One or both probes not found, symbol(s) queried instead.

Probe Symbol Probe Symbol Classification *Classification Classification Williamson Davicioni Exon

213832 at KCND3 226506 at THSD4 99.0 93.7 98.7 218184 at TULP4 202748 at GBP2 99.0 93.0 ··· 225306 s at SLC25A29 214719 at SLC46A3 99.0 ··· 96.3 202534 x at DHFR 224428 s at CDCA7 96.0 ··· ··· 212390 at PDE4DIP 209242 at PEG3 96.0 87.4 95.1 1569872 a at LMF1 201329 s at ETS2 96.0 70.6 75.3 204262 s at PSEN2 200844 s at PRDX6 96.0 87.4 87.7 208635 x at NACA 200949 x at RPS20 95.0 85.3 75.3 235066 at MAP4 219370 at RPRM 95.0 75.5 75.3 206373 at ZIC1 209242 at PEG3 95.0 92.3 93.8 228790 at FAM110B 209242 at PEG3 95.0 94.4 93.8 239466 at LOC344595 203481 at FAM178A 95.0 ··· ··· 213782 s at MYOZ2 205163 at MYLPF 95.0 88.8 90.1 208195 at TTN 205163 at MYLPF 95.0 96.5 90.1 213170 at GPX7 203625 x at SKP2 95.0 85.3 92.6 213170 at GPX7 211042 x at MCAM 95.0 85.3 81.5 213170 at GPX7 209242 at PEG3 95.0 88.8 93.8 1569685 at NA 212387 at TCF4 95.0 ··· ··· 212390 at PDE4DIP 202674 s at LMO7 95.0 83.2 95.1 239678 at NA 219370 at RPRM 95.0 ··· ··· 239678 at NA 200844 s at PRDX6 95.0 ··· ··· 218829 s at CHD7 203787 at SSBP2 95.0 83.2 ··· 218829 s at CHD7 230927 at NA 95.0 ··· ··· 219855 at NUDT11 229371 at NA 95.0 ··· ··· 227984 at LMF1 211421 s at RET 95.0 62.2 75.3 211373 s at PSEN2 235471 at VSTM4 95.0 ··· ··· 1557014 a at FAM201A 211421 s at RET 95.0 ··· ··· 209757 s at MYCN 200878 at EPAS1 95.0 89.5 93.8 209757 s at MYCN 242868 at NA 95.0 ··· ··· 227756 at FAM81A 242775 at PTGR1 95.0 ··· 96.3 1558801 at NA 224743 at IMPAD1 95.0 ··· ··· 204262 s at PSEN2 236141 at NBLA00301 95.0 81.8 85.2 242119 at PROX1 201940 at CPD 95.0 82.5 96.3 232796 at NA 203448 s at TERF1 95.0 ··· ··· 232796 at NA 203753 at TCF4 95.0 ··· ··· 214180 at MAN1C1 221910 at ETV1 95.0 79.7 85.2

71 SUPPLEMENTARY TABLE 5 Tumor sample characteristics

Sample Histological Fusion Percent Percent Subtype Status Tumor Necrosis 509 Alveolar Positive 100 0 4463 Alveolar Positive 90 10 22707 Alveolar Positive NA NA 12251AP Alveolar Positive NA NA 2369 Alveolar Positive 100 0 12251 Alveolar Positive 90 10 13413 Alveolar Positive 100 0 24130 Alveolar Positive 50 50 6468 Alveolar Negative 100 0 10191 Alveolar Negative 100 0 15438 Alveolar Negative 100 0 IRS73 Embryonal Positive 75 0 IRS93 Embryonal Positive 75 0 6152 Embryonal Negative 100 0 10012 Embryonal Negative NA NA 10440 Embryonal Negative NA NA 2574 Embryonal Negative 100 0 6237 Embryonal Negative 100 0 12240 Embryonal Negative NA NA IRS12 Embryonal Negative 80 0 IRS44 Embryonal Negative 80 20 IRS58 Embryonal Negative 95 0 IRS66 Embryonal Negative 90 10 IRS78 Embryonal Negative 80 0 IRS83 Embryonal Negative 80 10 IRS135 Embryonal Negative 90 0 IRS136 Embryonal Negative 100 0

72 SUPPLEMENTARY TABLE 6 Genes in nCounter set

Probe ID Gene ID Symbol Description 204567 s at NM 004915 ABCG1 ATP-binding cassette, sub-family G (WHITE), member 1 208212 s at NM 004304 ALK anaplastic lymphoma receptor tyrosine kinase 220326 s at NM 018071 ARHGEF40 Rho guanine nucleotide exchange factor (GEF) 40 221039 s at NM 018482 ASAP1 ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 207076 s at NM 000050 ASS1 argininosuccinate synthase 1 202715 at NM 004341 CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 206446 s at NM 001971 CELA2A/2B chymotrypsin-like elastase family, member 2A/2B 213436 at U73304 CNR1 cannabinoid receptor 1 (brain) 201639 s at NM 013291 CPSF1 cleavage and polyadenylation specific factor 1, 160kDa 203139 at NM 004938 DAPK1 death-associated protein kinase 1 221539 at AB044548 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 203678 at NM 014967 FAN1 FANCD2/FANCI-associated nuclease 1 203184 at NM 001999 FBN2 fibrillin 2 203706 s at NM 003507 FZD7 frizzled family receptor 7 217788 s at NM 004481 GALNT2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 213170 at AA406605 GPX7 glutathione peroxidase 7 208025 s at NM 003483 HMGA2 high mobility group AT-hook 2 206858 s at NM 004503 HOXC6 homeobox C6 203298 s at NM 004973 JARID2 jumonji, AT rich interactive domain 2 213478 at AB028949 KAZN kazrin, periplakin interacting protein 213832 at AA530995 KCND3 potassium voltage-gated channel, Shal-related subfamily, member 3 215014 at AL512727 KCND3 potassium voltage-gated channel, Shal-related subfamily, member 3 208767 s at AW149681 LAPTM4B lysosomal protein transmembrane 4 beta 206144 at NM 004742 MAGI1 membrane associated guanylate kinase, WW and PDZ domain containing 1 203417 at NM 017459 MFAP2 microfibrillar-associated protein 2 206089 at NM 006157 NELL1 NEL-like 1 (chicken) 204105 s at NM 005010 NRCAM neuronal cell adhesion molecule 218625 at NM 016588 NRN1 neuritin 1 203228 at NM 002573 PAFAH1B3 platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa) 219225 at NM 024554 PGBD5 piggyBac transposable element derived 5 201121 s at NM 006667 PGRMC1 progesterone receptor membrane component 1 221605 s at AF136970 PIPOX pipecolic acid oxidase 218613 at NM 018422 PSD3 pleckstrin and Sec7 domain containing 3 218683 at NM 021190 PTBP2 polypyrimidine tract binding protein 2 213280 at AK000478 RAP1GAP2 RAP1 GTPase activating protein 2 211686 s at AF251062 RBM13/MAK16 MAK16 homolog (S. cerevisiae) 217946 s at NM 016402 SAE1 SUMO1 activating enzyme subunit 1 218974 at NM 018013 SOBP sine oculis binding protein homolog (Drosophila) 212458 at H97931 SPRED2 sprouty-related, EVH1 domain containing 2 204743 at NM 013259 TAGLN3 transgelin 3 214451 at NM 003221 TFAP2B transcription factor AP-2 beta (activating enhancer binding protein 2 beta) 216623 x at AK025084 TOX3 TOX high mobility group box family member 3 218502 s at NM 014112 TRPS1 trichorhinophalangeal syndrome I 218184 at NM 020245 TULP4 tubby like protein 4 213155 at AB011095 WSCD1 WSC domain containing 1 206373 at NM 003412 ZIC1 Zic family member 1

73 SUPPLEMENTARY TABLE 7 PCA Scores by tumor sample for nCounter Data

Sample Fusion PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 509 Pos 13.062 5.811 5.213 -2.882 0.292 -0.039 0.228 -0.293 0.077 -0.283 4463 Pos 4.734 -0.692 -0.598 0.206 0.540 0.849 0.120 0.245 1.055 1.705 6152 Neg -4.035 8.610 -1.425 -1.550 -0.618 0.812 -2.994 0.937 -1.459 -0.602 10012 Neg -4.821 4.267 -1.531 -1.631 0.663 3.141 0.715 -2.369 0.811 0.810 10440 Neg -6.350 9.193 -0.752 0.306 1.836 -1.923 2.042 0.172 0.289 -0.020 22707 Pos 8.727 2.046 -3.661 2.351 0.287 -1.791 -2.196 -1.737 1.211 -0.370 12251AP Pos 5.091 -0.083 -2.827 0.237 -1.787 0.485 1.608 0.477 -1.344 -0.186 2369 Pos 4.237 0.712 -1.142 0.441 -0.853 -0.207 0.267 0.890 -0.314 1.013 2574 Neg -3.269 1.981 0.228 0.007 -1.755 -1.095 0.660 0.501 1.251 -1.076 6237 Neg -1.683 0.268 0.817 1.291 -0.263 -0.365 1.192 -0.717 -0.173 -1.289 6468 Neg -1.688 -1.909 0.417 -0.192 -1.390 0.895 -0.210 0.597 1.340 1.045 10191 Neg -3.085 0.810 1.405 0.321 -1.999 -0.501 -0.520 1.485 1.261 -0.084 12240 Neg -2.509 1.748 3.849 4.970 -1.332 1.106 -0.569 -1.128 -1.317 0.421 12251 Pos 4.754 -0.329 -2.349 0.089 -1.342 0.643 1.621 0.538 -1.365 0.055 13413 Pos 2.029 0.328 0.061 2.598 4.262 1.128 0.173 2.053 0.187 -0.237 15438 Neg -1.881 -0.963 -0.199 -0.398 -0.568 0.949 -0.515 1.376 0.884 -0.164 24130 Pos -0.168 -2.765 0.269 0.507 -0.429 0.998 0.340 -0.742 1.151 -1.606 IRS.12 Neg -1.236 -3.478 0.110 -0.706 0.361 -0.297 -0.506 0.226 -0.311 0.096 IRS.44 Neg -1.004 -4.863 -0.135 -1.175 0.228 -0.092 -0.110 -0.407 -0.222 -0.695 IRS.58 Neg -2.088 -2.267 0.448 -0.632 0.296 -0.975 -0.799 0.031 -0.238 1.487 IRS.66 Neg -2.512 -0.507 0.668 -0.088 -0.434 -2.188 0.711 -0.608 -0.148 1.506 IRS.73 Pos 0.562 -3.361 -0.292 -0.467 0.357 0.368 0.194 -0.121 -0.217 -0.989 IRS.78 Neg -2.449 -1.574 -0.198 -1.872 0.776 -0.913 -0.236 -0.678 -0.913 -0.226 IRS.83 Neg -1.932 -2.909 0.347 -0.922 0.516 -0.249 -0.063 -0.068 -0.047 -0.158 IRS.93 Pos 0.365 -4.013 0.142 -0.560 0.448 -0.116 -0.352 -0.191 0.174 -0.391 IRS.135 Neg -1.208 -3.330 0.731 -0.064 1.398 -0.035 -0.377 -0.020 -0.796 -0.172 IRS.136 Neg -1.643 -2.732 0.404 -0.184 0.507 -0.588 -0.423 -0.450 -0.828 0.411

74 SUPPLEMENTARY TABLE 8 PCA Loadings for nCounter Data

Probe ID Symbol PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 204567 s at ABCG1 0.192 0.102 0.196 -0.113 0.050 -0.034 0.031 -0.032 0.053 -0.044 213832 at AF070632 0.204 0.055 -0.145 0.154 0.045 0.006 -0.012 0.068 -0.007 0.144 208212 s at ALK 0.180 0.093 0.244 -0.174 0.065 0.014 0.091 -0.013 -0.018 -0.056 207076 s at ASS 0.202 0.054 -0.153 0.044 -0.046 0.099 0.211 0.114 -0.167 0.023 215014 at AW819521 0.202 0.096 0.122 -0.124 -0.003 -0.078 -0.027 -0.102 0.045 -0.035 202715 at CAD -0.076 0.203 -0.049 0.294 0.086 0.176 0.164 0.079 -0.067 0.054 213436 at CNR1 0.174 0.065 -0.105 0.130 0.067 -0.165 -0.279 -0.283 0.316 0.059 201639 s at CPSF1 -0.032 0.225 -0.110 -0.115 -0.183 0.077 -0.251 0.250 -0.113 -0.098 203139 at DAPK1 0.195 0.118 0.029 -0.044 0.059 -0.030 -0.102 0.014 0.137 -0.022 221039 s at DDEF1 -0.057 0.245 -0.064 -0.088 -0.052 0.224 -0.185 0.099 -0.038 -0.059 221539 at EIF4EBP1 -0.067 0.222 -0.019 -0.184 -0.030 0.261 -0.022 -0.245 0.029 0.168 206446 s at ELA2A 0.210 0.082 0.004 0.037 0.085 -0.070 -0.113 -0.118 0.206 0.020 203184 at FBN2 -0.118 0.159 -0.120 -0.199 0.114 0.219 -0.008 -0.380 -0.037 0.163 218974 at FLJ10159 -0.100 0.186 0.020 0.012 -0.185 0.171 0.022 -0.049 0.217 0.341 220326 s at FLJ10357 -0.076 0.180 -0.029 -0.058 0.332 -0.351 0.048 -0.103 -0.174 0.181 203706 s at FZD7 -0.076 0.079 0.262 0.083 -0.321 -0.338 -0.108 0.139 0.114 0.261 217788 s at GALNT2 -0.092 0.175 0.033 0.150 -0.202 0.323 0.020 -0.263 0.167 -0.255 213170 at GPX7 -0.079 0.193 -0.233 -0.060 0.158 0.153 0.205 0.107 0.087 0.053 208025 s at HMGA2 -0.142 0.165 -0.048 -0.107 0.110 -0.292 0.231 -0.091 0.018 -0.058 206858 s at HOXC6 -0.132 0.174 0.126 0.101 0.050 -0.112 -0.070 -0.096 -0.282 0.302 203298 s at JARID2 0.194 0.124 0.026 -0.012 -0.054 0.010 0.215 0.022 -0.115 -0.038 213155 at KIAA0523 0.217 0.073 -0.076 0.049 0.086 -0.042 -0.031 0.032 0.070 0.025 203678 at KIAA1018 0.117 0.031 -0.240 -0.050 -0.411 -0.215 0.089 -0.208 -0.093 -0.278 213478 at KIAA1026 -0.111 0.164 0.244 0.228 -0.065 -0.135 -0.096 0.044 -0.133 -0.070 208767 s at LAPTM4B -0.078 0.201 0.111 -0.009 -0.205 0.061 -0.148 0.299 0.267 0.049 213280 at LOC653127 0.160 0.083 0.141 0.176 0.308 0.149 -0.097 0.051 0.032 -0.170 218613 at LOC653754 -0.126 0.202 -0.021 -0.082 -0.038 -0.126 -0.090 0.117 0.080 -0.029 206144 at MAGI1 0.177 0.108 0.248 -0.089 0.076 -0.007 0.010 -0.166 0.096 -0.049 203417 at MFAP2 -0.110 0.173 -0.053 -0.003 -0.081 -0.134 0.373 -0.112 0.282 -0.221 206089 at NELL1 0.199 0.096 0.021 -0.013 -0.050 0.045 0.184 0.149 -0.174 0.047 204105 s at NRCAM 0.158 0.089 -0.273 0.054 -0.077 -0.107 -0.342 -0.059 -0.066 0.035 218625 at NRN1 0.177 0.053 -0.033 0.062 0.025 0.050 0.180 0.088 0.129 0.473 203228 at PAFAH1B3 -0.049 0.210 -0.064 -0.250 -0.116 -0.175 -0.078 -0.044 -0.216 -0.066 219225 at PGBD5 0.196 0.115 0.104 -0.153 -0.018 -0.044 -0.039 -0.056 -0.016 -0.016 201121 s at PGRMC1 -0.129 0.163 -0.007 0.158 -0.003 -0.197 0.311 0.089 0.271 -0.078 221605 s at PIPOX 0.165 0.039 -0.251 0.231 0.162 -0.051 -0.116 -0.032 0.117 -0.148 218683 at PTBP2 0.086 0.104 0.296 0.310 -0.245 0.130 0.028 -0.223 -0.183 -0.042 211686 s at RBM13/MAK16 -0.021 0.246 -0.166 0.029 0.067 -0.021 -0.050 0.274 0.080 -0.081 217946 s at SAE1 0.083 0.192 0.232 -0.062 0.218 0.052 -0.003 0.237 -0.099 -0.238 212458 at SPRED2 -0.125 0.197 -0.063 0.004 0.114 0.033 -0.125 0.009 -0.150 -0.090 204743 at TAGLN3 0.196 0.071 -0.147 0.077 -0.185 -0.024 0.063 -0.023 -0.170 0.065 214451 at TFAP2B 0.200 0.061 -0.156 0.073 -0.142 0.016 0.165 0.014 -0.207 0.072 216623 x at TNRC9 0.184 0.086 0.197 -0.213 -0.032 0.037 0.087 -0.025 -0.003 0.042 218502 s at TRPS1 -0.142 0.193 -0.072 -0.072 0.101 -0.077 -0.041 -0.111 -0.104 -0.045 218184 at TULP4 0.205 0.099 -0.110 0.008 -0.072 -0.061 0.014 0.091 0.073 0.050 206373 at ZIC1 -0.077 0.145 0.063 0.469 0.097 -0.067 -0.018 -0.144 -0.143 -0.032

75 SUPPLEMENTARY TABLE 9 Top-scoring nCounter dyad classifiers

Probe Symbol Probe Symbol Classiﬁcation Classiﬁcation nCounter Williamson 202715 at CAD 221605 s at PIPOX 100 97.0 213436 at CNR1 203706 s at FZD7 100 97.0 203139 at DAPK1 203184 at FBN2 100 94.1 203139 at DAPK1 218974 at FLJ10159 100 92.1 203139 at DAPK1 203706 s at FZD7 100 93.1 203139 at DAPK1 208025 s at HMGA2 100 91.1 203139 at DAPK1 206858 s at HOXC6 100 91.1 203139 at DAPK1 213478 at KAZN/KIAA1026 100 94.1 203139 at DAPK1 208767 s at LAPTM4B 100 89.1 203139 at DAPK1 218613 at LOC653754 100 92.1 203139 at DAPK1 212458 at SPRED2 100 95.0 203139 at DAPK1 218502 s at TRPS1 100 95.0 221539 at EIF4EBP1 221605 s at PIPOX 100 97.0 218974 at FLJ10159 221605 s at PIPOX 100 96.0 208025 s at HMGA2 221605 s at PIPOX 100 97.0 206858 s at HOXC6 213280 at LOC653127 100 94.1 206858 s at HOXC6 221605 s at PIPOX 100 98.0 208767 s at LAPTM4B 221605 s at PIPOX 100 97.0 203228 at PAFAH1B3 221605 s at PIPOX 100 97.0 203228 at PAFAH1B3 216623 x at TOX3 100 88.1 221605 s at PIPOX 211686 s at RBM13 100 98.0 221605 s at PIPOX 217946 s at SAE1 100 96.0 221605 s at PIPOX 206373 at ZIC1 100 96.0

76 SUPPLEMENTARY TABLE 10 Top gene combinations - Lung Cancer Data

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216468 s at ZNF682 205839 s at BZRAP1 98.3 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 218995 s at EDN1 216468 s at ZNF682 98.3 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 216468 s at ZNF682 220584 at FLJ22184 98.3 203068 at KLHL21 216533 at PCCA 218995 s at EDN1 216468 s at ZNF682 220584 at FLJ22184 98.3 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 217946 s at SAE1 96.6 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 221937 at SYNRG 96.6 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 218922 s at CERS4 96.6 209371 s at SH3BP2 200875 s at MIR1292 221937 at SYNRG 203009 at BCAM 96.6 209371 s at SH3BP2 203068 at KLHL21 221827 at RBCK1 220788 s at IRF9 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216533 at PCCA 216468 s at ZNF682 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216533 at PCCA 211163 s at TNFRSF10C 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 217831 s at NSFL1C 205244 s at SLC13A3 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 218995 s at EDN1 205244 s at SLC13A3 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 218995 s at EDN1 211685 s at NCALD 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 218995 s at EDN1 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 205244 s at SLC13A3 216468 s at ZNF682 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 205244 s at SLC13A3 207237 at KCNA3 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 211685 s at NCALD 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 209125 at KRT6A 218995 s at EDN1 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 214772 at C11orf41 211685 s at NCALD 96.6 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 216533 at PCCA 216468 s at ZNF682 96.6 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 216468 s at ZNF682 220082 at PPP1R14D 96.6 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 216468 s at ZNF682 207237 at KCNA3 96.6 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 209825 s at MIR3658 220082 at PPP1R14D 96.6 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 217831 s at NSFL1C 220584 at FLJ22184 96.6 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 216468 s at ZNF682 220584 at FLJ22184 96.6 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 211685 s at NCALD 220584 at FLJ22184 96.6

77 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 220584 at FLJ22184 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 216468 s at ZNF682 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 201250 s at SLC2A1 207237 at KCNA3 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 209825 s at MIR3658 207237 at KCNA3 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 217831 s at NSFL1C 216468 s at ZNF682 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 218995 s at EDN1 205839 s at BZRAP1 211417 x at GGT1 96.6 209371 s at SH3BP2 200875 s at MIR1292 205244 s at SLC13A3 216468 s at ZNF682 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 211685 s at NCALD 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 220584 at FLJ22184 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 211163 s at TNFRSF10C 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 220082 at PPP1R14D 207237 at KCNA3 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 204909 at DDX6 214033 at ABCC6 205839 s at BZRAP1 96.6 209371 s at SH3BP2 200875 s at MIR1292 207237 at KCNA3 211685 s at NCALD 211163 s at TNFRSF10C 96.6 209371 s at SH3BP2 200875 s at MIR1292 214033 at ABCC6 211163 s at TNFRSF10C 205839 s at BZRAP1 96.6 203068 at KLHL21 202234 s at SLC16A1 216533 at PCCA 218995 s at EDN1 216468 s at ZNF682 96.6 203068 at KLHL21 216533 at PCCA 218995 s at EDN1 216468 s at ZNF682 220082 at PPP1R14D 96.6 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 213050 at COBL 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 220788 s at IRF9 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 203717 at DPP4 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 201379 s at TPD52L2 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 213050 at COBL 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 203009 at BCAM 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 218922 s at CERS4 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 209919 x at GGT1 94.9 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 207131 x at GGT1 94.9 209371 s at SH3BP2 200875 s at MIR1292 201250 s at SLC2A1 213050 at COBL 94.9 209371 s at SH3BP2 200875 s at MIR1292 201250 s at SLC2A1 220584 at FLJ22184 94.9

78 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 209825 s at MIR3658 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 218995 s at EDN1 203009 at BCAM 94.9 209371 s at SH3BP2 200875 s at MIR1292 218995 s at EDN1 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 220788 s at IRF9 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 217117 x at MUC3A 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 203716 s at DPP4 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 205378 s at ACHE 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 219135 s at LMF1 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 216468 s at ZNF682 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 220082 at PPP1R14D 94.9 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 205229 s at COCH 203749 s at RARA 94.9 209371 s at SH3BP2 200875 s at MIR1292 220788 s at IRF9 203749 s at RARA 94.9 209371 s at SH3BP2 200875 s at MIR1292 220788 s at IRF9 207237 at KCNA3 94.9 209371 s at SH3BP2 200875 s at MIR1292 220788 s at IRF9 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 65438 at KIAA1609 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 221937 at SYNRG 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 208997 s at UCP2 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 215110 at LOC100288974 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 211423 s at SC5DL 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203009 at BCAM 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 202420 s at DHX9 203749 s at RARA 94.9 209371 s at SH3BP2 200875 s at MIR1292 205975 s at HOXD1 203749 s at RARA 94.9 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 214033 at ABCC6 205839 s at BZRAP1 94.9 209371 s at SH3BP2 203068 at KLHL21 220788 s at IRF9 210014 x at IDH3B 94.9 209371 s at SH3BP2 216805 at — 214772 at C11orf41 203785 s at DDX28 94.9 209371 s at SH3BP2 216805 at — 215653 at — 203785 s at DDX28 94.9

79 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 214772 at C11orf41 221827 at RBCK1 211416 x at GGTLC1 94.9 209371 s at SH3BP2 201250 s at SLC2A1 221827 at RBCK1 220788 s at IRF9 94.9 209371 s at SH3BP2 208433 s at LRP8 210014 x at IDH3B 204687 at PARM1 94.9 209371 s at SH3BP2 215653 at — 221827 at RBCK1 211416 x at GGTLC1 94.9 209371 s at SH3BP2 204033 at TRIP13 221827 at RBCK1 216468 s at ZNF682 94.9 209371 s at SH3BP2 221827 at RBCK1 220788 s at IRF9 211478 s at DPP4 94.9 209125 at KRT6A 213050 at COBL 220550 at FBXO4 208025 s at HMGA2 94.9 216533 at PCCA 218995 s at EDN1 216468 s at ZNF682 214088 s at FUT3 94.9 216533 at PCCA 218995 s at EDN1 214088 s at FUT3 211163 s at TNFRSF10C 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 203068 at KLHL21 205839 s at BZRAP1 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 201250 s at SLC2A1 220584 at FLJ22184 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 215457 at — 220584 at FLJ22184 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 209825 s at MIR3658 220584 at FLJ22184 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 207717 s at PKP2 220584 at FLJ22184 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 216468 s at ZNF682 205839 s at BZRAP1 94.9 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 214033 at ABCC6 205839 s at BZRAP1 94.9 209371 s at SH3BP2 205490 x at GJB3 216805 at — 214772 at C11orf41 209825 s at MIR3658 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 203068 at KLHL21 205839 s at BZRAP1 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 216805 at — 220584 at FLJ22184 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 214772 at C11orf41 218922 s at CERS4 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 201250 s at SLC2A1 220584 at FLJ22184 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 216533 at PCCA 205839 s at BZRAP1 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 209825 s at MIR3658 220584 at FLJ22184 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 218995 s at EDN1 220584 at FLJ22184 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 218995 s at EDN1 205839 s at BZRAP1 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 216468 s at ZNF682 205839 s at BZRAP1 94.9

80 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 207237 at KCNA3 205839 s at BZRAP1 94.9 209371 s at SH3BP2 220658 s at ARNTL2 200875 s at MIR1292 214033 at ABCC6 205839 s at BZRAP1 94.9 209371 s at SH3BP2 205282 at LRP8 200875 s at MIR1292 203068 at KLHL21 205839 s at BZRAP1 94.9 209371 s at SH3BP2 205282 at LRP8 200875 s at MIR1292 214772 at C11orf41 218922 s at CERS4 94.9 209371 s at SH3BP2 205282 at LRP8 200875 s at MIR1292 208453 s at XPNPEP1 207237 at KCNA3 94.9 209371 s at SH3BP2 205282 at LRP8 200875 s at MIR1292 211163 s at TNFRSF10C 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 209125 at KRT6A 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216805 at — 214772 at C11orf41 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216805 at — 216533 at PCCA 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216805 at — 216468 s at ZNF682 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216805 at — 207237 at KCNA3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216805 at — 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 214772 at C11orf41 216533 at PCCA 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 214772 at C11orf41 205244 s at SLC13A3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 208453 s at XPNPEP1 207237 at KCNA3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 208453 s at XPNPEP1 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 215457 at — 207237 at KCNA3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 215457 at — 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 202234 s at SLC16A1 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 202234 s at SLC16A1 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216533 at PCCA 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207717 s at PKP2 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207717 s at PKP2 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 217831 s at NSFL1C 207237 at KCNA3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 217831 s at NSFL1C 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 217831 s at NSFL1C 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 219491 at LRFN4 218922 s at CERS4 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 219491 at LRFN4 205839 s at BZRAP1 94.9

81 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 216468 s at ZNF682 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 218922 s at CERS4 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 204753 s at HLF 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 214088 s at FUT3 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 220584 at FLJ22184 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 211685 s at NCALD 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 214033 at ABCC6 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 215440 s at BEX4 205839 s at BZRAP1 94.9 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 214088 s at FUT3 205839 s at BZRAP1 94.9 202087 s at CTSL1 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 94.1 209371 s at SH3BP2 37966 at PARVB 209126 x at KRT6B 211685 s at NCALD 94.1 209371 s at SH3BP2 204992 s at PFN2 46665 at SEMA4C 203509 at SORL1 94.1 209371 s at SH3BP2 204992 s at PFN2 205244 s at SLC13A3 203509 at SORL1 94.1 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 215603 x at GGT1 94.1 209371 s at SH3BP2 208308 s at GPI 203215 s at MYO6 211685 s at NCALD 94.1 209371 s at SH3BP2 208308 s at GPI 202420 s at DHX9 211685 s at NCALD 94.1 202233 s at UQCRH 215457 at — 206744 s at ZMYM5 214033 at ABCC6 94.1 216805 at — 214772 at C11orf41 202341 s at TRIM2 211685 s at NCALD 94.1 210213 s at EIF6 205244 s at SLC13A3 202341 s at TRIM2 209919 x at GGT1 94.1 209371 s at SH3BP2 205490 x at GJB3 200875 s at MIR1292 203749 s at RARA 93.2 209371 s at SH3BP2 205490 x at GJB3 213050 at COBL 220788 s at IRF9 93.2 209371 s at SH3BP2 205282 at LRP8 200875 s at MIR1292 218995 s at EDN1 93.2 209371 s at SH3BP2 205282 at LRP8 216805 at — 217946 s at SAE1 93.2 209371 s at SH3BP2 205282 at LRP8 221827 at RBCK1 211423 s at SC5DL 93.2 209371 s at SH3BP2 205282 at LRP8 210014 x at IDH3B 204687 at PARM1 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 209825 s at MIR3658 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 202233 s at UQCRH 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 205528 s at RUNX1T1 93.2

82 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 40837 at TLE2 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 220108 at GNA14 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 211478 s at DPP4 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 203009 at BCAM 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 207237 at KCNA3 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 220584 at FLJ22184 93.2 209371 s at SH3BP2 200875 s at MIR1292 209125 at KRT6A 213050 at COBL 93.2 209371 s at SH3BP2 200875 s at MIR1292 209125 at KRT6A 215110 at LOC100288974 93.2 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 208453 s at XPNPEP1 93.2 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 220788 s at IRF9 93.2 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 203785 s at DDX28 93.2 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 203009 at BCAM 93.2 209371 s at SH3BP2 200875 s at MIR1292 216805 at — 216468 s at ZNF682 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 208453 s at XPNPEP1 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 40837 at TLE2 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 207559 s at ZMYM3 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 216468 s at ZNF682 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 220584 at FLJ22184 93.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 211416 x at GGTLC1 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 202233 s at UQCRH 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 220788 s at IRF9 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 221937 at SYNRG 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 215110 at LOC100288974 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 203749 s at RARA 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 221249 s at FAM117A 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 207237 at KCNA3 93.2 209371 s at SH3BP2 200875 s at MIR1292 208453 s at XPNPEP1 220584 at FLJ22184 93.2 209371 s at SH3BP2 200875 s at MIR1292 202234 s at SLC16A1 220584 at FLJ22184 93.2

83 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 216533 at PCCA 215945 s at TRIM2 93.2 209371 s at SH3BP2 200875 s at MIR1292 216533 at PCCA 216468 s at ZNF682 93.2 209371 s at SH3BP2 200875 s at MIR1292 216533 at PCCA 211163 s at TNFRSF10C 93.2 209371 s at SH3BP2 200875 s at MIR1292 216533 at PCCA 205839 s at BZRAP1 93.2 209371 s at SH3BP2 200875 s at MIR1292 203068 at KLHL21 202580 x at FOXM1 93.2 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 202580 x at FOXM1 93.2 220658 s at ARNTL2 210213 s at EIF6 205244 s at SLC13A3 202341 s at TRIM2 92.6 205490 x at GJB3 202234 s at SLC16A1 204992 s at PFN2 206744 s at ZMYM5 92.6 205490 x at GJB3 209371 s at SH3BP2 204992 s at PFN2 218996 at TFPT 92.6 205490 x at GJB3 209371 s at SH3BP2 208308 s at GPI 211685 s at NCALD 92.6 205490 x at GJB3 37966 at PARVB 214772 at C11orf41 205244 s at SLC13A3 92.6 205490 x at GJB3 37966 at PARVB 214772 at C11orf41 207559 s at ZMYM3 92.6 205490 x at GJB3 37966 at PARVB 214772 at C11orf41 218922 s at CERS4 92.6 205490 x at GJB3 206744 s at ZMYM5 213599 at OIP5 214033 at ABCC6 92.6 208453 s at XPNPEP1 202234 s at SLC16A1 209371 s at SH3BP2 204992 s at PFN2 92.6 205282 at LRP8 216805 at — 206744 s at ZMYM5 214033 at ABCC6 92.6 205282 at LRP8 216805 at — 216468 s at ZNF682 211423 s at SC5DL 92.6 201250 s at SLC2A1 202234 s at SLC16A1 209371 s at SH3BP2 216342 x at — 92.6 201250 s at SLC2A1 209371 s at SH3BP2 209900 s at SLC16A1 216342 x at — 92.6 201250 s at SLC2A1 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 92.6 201250 s at SLC2A1 209371 s at SH3BP2 218996 at TFPT 211685 s at NCALD 92.6 201250 s at SLC2A1 209371 s at SH3BP2 208308 s at GPI 211685 s at NCALD 92.6 201250 s at SLC2A1 209371 s at SH3BP2 220865 s at PDSS1 216342 x at — 92.6 201250 s at SLC2A1 204992 s at PFN2 211379 x at B3GALNT1 211423 s at SC5DL 92.6 201250 s at SLC2A1 211379 x at B3GALNT1 203749 s at RARA 214033 at ABCC6 92.6 201250 s at SLC2A1 46142 at LMF1 205244 s at SLC13A3 220584 at FLJ22184 92.6 202234 s at SLC16A1 202087 s at CTSL1 209371 s at SH3BP2 203509 at SORL1 92.6 202234 s at SLC16A1 209371 s at SH3BP2 209709 s at HMMR 203509 at SORL1 92.6

84 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 202234 s at SLC16A1 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 92.6 202234 s at SLC16A1 209371 s at SH3BP2 203509 at SORL1 203009 at BCAM 92.6 209825 s at MIR3658 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 92.6 209825 s at MIR3658 209371 s at SH3BP2 211379 x at B3GALNT1 203509 at SORL1 92.6 209825 s at MIR3658 215243 s at GJB3 202420 s at DHX9 205244 s at SLC13A3 92.6 209825 s at MIR3658 208878 s at PAK2 203749 s at RARA 214033 at ABCC6 92.6 219491 at LRFN4 204033 at TRIP13 206744 s at ZMYM5 46665 at SEMA4C 92.6 202087 s at CTSL1 209371 s at SH3BP2 217398 x at GAPDH 211423 s at SC5DL 92.6 202087 s at CTSL1 209371 s at SH3BP2 210213 s at EIF6 203274 at F8A1 92.6 202087 s at CTSL1 212295 s at SLC7A1 203749 s at RARA 214033 at ABCC6 92.6 202087 s at CTSL1 214772 at C11orf41 219374 s at ALG9 211163 s at TNFRSF10C 92.6 209371 s at SH3BP2 37966 at PARVB 204033 at TRIP13 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 209125 at KRT6A 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 212581 x at GAPDH 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 202236 s at SLC16A1 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 205085 at ORC1 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 204992 s at PFN2 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 208308 s at GPI 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 217967 s at FAM129A 216659 at LOC1720 92.6 209371 s at SH3BP2 37966 at PARVB 216659 at LOC1720 203274 at F8A1 92.6 209371 s at SH3BP2 37966 at PARVB 216342 x at — 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 216468 s at ZNF682 211685 s at NCALD 92.6 209371 s at SH3BP2 37966 at PARVB 203509 at SORL1 208284 x at GGT1 92.6 209371 s at SH3BP2 37966 at PARVB 211685 s at NCALD 209919 x at GGT1 92.6 209371 s at SH3BP2 37966 at PARVB 211685 s at NCALD 211417 x at GGT1 92.6 209371 s at SH3BP2 204855 at SERPINB5 204992 s at PFN2 203509 at SORL1 92.6 209371 s at SH3BP2 204855 at SERPINB5 203509 at SORL1 211685 s at NCALD 92.6 209371 s at SH3BP2 204033 at TRIP13 205378 s at ACHE 211423 s at SC5DL 92.6

85 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 204033 at TRIP13 203509 at SORL1 214033 at ABCC6 92.6 209371 s at SH3BP2 209125 at KRT6A 204992 s at PFN2 203509 at SORL1 92.6 209371 s at SH3BP2 204128 s at RFC3 212581 x at GAPDH 211423 s at SC5DL 92.6 209371 s at SH3BP2 215457 at — 216468 s at ZNF682 211685 s at NCALD 92.6 209371 s at SH3BP2 215457 at — 205975 s at HOXD1 211685 s at NCALD 92.6 209371 s at SH3BP2 212581 x at GAPDH 211379 x at B3GALNT1 203509 at SORL1 92.6 209371 s at SH3BP2 212581 x at GAPDH 203509 at SORL1 211423 s at SC5DL 92.6 209371 s at SH3BP2 212581 x at GAPDH 211685 s at NCALD 207131 x at GGT1 92.6 209371 s at SH3BP2 212581 x at GAPDH 211685 s at NCALD 215603 x at GGT1 92.6 209371 s at SH3BP2 202267 at LAMC2 204992 s at PFN2 211423 s at SC5DL 92.6 209371 s at SH3BP2 217398 x at GAPDH 211379 x at B3GALNT1 203509 at SORL1 92.6 209371 s at SH3BP2 217398 x at GAPDH 203348 s at ETV5 211685 s at NCALD 92.6 209371 s at SH3BP2 217398 x at GAPDH 220108 at GNA14 203509 at SORL1 92.6 209371 s at SH3BP2 217398 x at GAPDH 211685 s at NCALD 209919 x at GGT1 92.6 209371 s at SH3BP2 209126 x at KRT6B 204992 s at PFN2 203509 at SORL1 92.6 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 205839 s at BZRAP1 92.6 209371 s at SH3BP2 200875 s at MIR1292 203509 at SORL1 205839 s at BZRAP1 92.6 209371 s at SH3BP2 204992 s at PFN2 215243 s at GJB3 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 210213 s at EIF6 220584 at FLJ22184 92.6 209371 s at SH3BP2 204992 s at PFN2 211379 x at B3GALNT1 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 218996 at TFPT 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 205378 s at ACHE 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 213900 at FAM189A2 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 213437 at RUFY3 219374 s at ALG9 92.6 209371 s at SH3BP2 204992 s at PFN2 203217 s at ST3GAL5 203509 at SORL1 92.6 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 211163 s at TNFRSF10C 92.6 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 203009 at BCAM 92.6 209371 s at SH3BP2 204992 s at PFN2 203509 at SORL1 220584 at FLJ22184 92.6

86 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 211379 x at B3GALNT1 208308 s at GPI 211423 s at SC5DL 92.6 209371 s at SH3BP2 213453 x at GAPDH 211685 s at NCALD 207131 x at GGT1 92.6 209371 s at SH3BP2 203968 s at CDC6 218996 at TFPT 211685 s at NCALD 92.6 209371 s at SH3BP2 200875 s at MIR1292 220788 s at IRF9 91.5 209371 s at SH3BP2 200875 s at MIR1292 203749 s at RARA 91.5 209371 s at SH3BP2 216805 at — 203215 s at MYO6 91.5 209371 s at SH3BP2 221827 at RBCK1 220788 s at IRF9 91.5 209371 s at SH3BP2 203785 s at DDX28 205264 at CD3EAP 91.5 209371 s at SH3BP2 203785 s at DDX28 218670 at PUS1 91.5 209371 s at SH3BP2 200604 s at PRKAR1A 211416 x at GGTLC1 91.5 209371 s at SH3BP2 203215 s at MYO6 211685 s at NCALD 91.5 209125 at KRT6A 212877 at KLC1 219374 s at ALG9 91.5 214772 at C11orf41 221704 s at VPS37B 217257 at SH3BP2 91.5 206414 s at ASAP2 34449 at CASP2 208284 x at GGT1 91.5 221704 s at VPS37B 206744 s at ZMYM5 208284 x at GGT1 91.5 221704 s at VPS37B 215924 at — 202420 s at DHX9 91.5 220788 s at IRF9 215243 s at GJB3 203716 s at DPP4 91.5 201250 s at SLC2A1 55081 at MICALL1 203215 s at MYO6 91.2 202087 s at CTSL1 203749 s at RARA 214033 at ABCC6 91.2 209371 s at SH3BP2 37966 at PARVB 211685 s at NCALD 91.2 209371 s at SH3BP2 202702 at TRIM26 203509 at SORL1 91.2 209371 s at SH3BP2 211685 s at NCALD 215603 x at GGT1 91.2 215457 at — 201650 at KRT19 220584 at FLJ22184 91.2 203966 s at PPM1A 200933 x at RPS4X 220584 at FLJ22184 91.2 209838 at COPS2 215079 at — 202580 x at FOXM1 91.2 209371 s at SH3BP2 200875 s at MIR1292 214772 at C11orf41 89.8 209371 s at SH3BP2 200875 s at MIR1292 213050 at COBL 89.8 209371 s at SH3BP2 200875 s at MIR1292 209049 s at ZMYND8 89.8

87 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 200875 s at MIR1292 209045 at XPNPEP1 89.8 209371 s at SH3BP2 200875 s at MIR1292 202046 s at ARHGAP35 89.8 209371 s at SH3BP2 200875 s at MIR1292 216375 s at ETV5 89.8 209371 s at SH3BP2 200875 s at MIR1292 40837 at TLE2 89.8 209371 s at SH3BP2 200875 s at MIR1292 221687 s at FAM125B 89.8 209371 s at SH3BP2 200875 s at MIR1292 220425 x at ROPN1B 89.8 209371 s at SH3BP2 200875 s at MIR1292 216468 s at ZNF682 89.8 209371 s at SH3BP2 200875 s at MIR1292 204909 at DDX6 89.8 209371 s at SH3BP2 200875 s at MIR1292 218922 s at CERS4 89.8 209371 s at SH3BP2 200875 s at MIR1292 211163 s at TNFRSF10C 89.8 209371 s at SH3BP2 200875 s at MIR1292 205839 s at BZRAP1 89.8 209371 s at SH3BP2 203068 at KLHL21 216659 at LOC1720 89.8 209371 s at SH3BP2 203068 at KLHL21 207559 s at ZMYM3 89.8 209371 s at SH3BP2 209125 at KRT6A 211994 at WNK1 89.8 209371 s at SH3BP2 216805 at — 203785 s at DDX28 89.8 209371 s at SH3BP2 216805 at — 211994 at WNK1 89.8 209371 s at SH3BP2 215457 at — 201650 at KRT19 89.8 209371 s at SH3BP2 209825 s at MIR3658 203509 at SORL1 89.8 209371 s at SH3BP2 209825 s at MIR3658 206859 s at PAEP 89.8 209371 s at SH3BP2 209825 s at MIR3658 211685 s at NCALD 89.8 209371 s at SH3BP2 203602 s at ZBTB17 214260 at COPS8 89.8 209371 s at SH3BP2 37966 at PARVB 216659 at LOC1720 89.8 209371 s at SH3BP2 221827 at RBCK1 210092 at MAGOH 89.8 209371 s at SH3BP2 221827 at RBCK1 211373 s at PSEN2 89.8 209371 s at SH3BP2 221827 at RBCK1 204687 at PARM1 89.8 209371 s at SH3BP2 221827 at RBCK1 211417 x at GGT1 89.8 209371 s at SH3BP2 221827 at RBCK1 211416 x at GGTLC1 89.8 209371 s at SH3BP2 210213 s at EIF6 202087 s at CTSL1 89.8

88 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 209371 s at SH3BP2 210213 s at EIF6 212877 at KLC1 89.8 209371 s at SH3BP2 210213 s at EIF6 218020 s at ZFAND3 89.8 209371 s at SH3BP2 220788 s at IRF9 203966 s at PPM1A 89.8 209371 s at SH3BP2 65438 at KIAA1609 203785 s at DDX28 89.8 209371 s at SH3BP2 65438 at KIAA1609 203509 at SORL1 89.8 209371 s at SH3BP2 203785 s at DDX28 214088 s at FUT3 89.8 209371 s at SH3BP2 210092 at MAGOH 200604 s at PRKAR1A 89.8 209371 s at SH3BP2 212877 at KLC1 204124 at SLC34A2 89.8 209371 s at SH3BP2 212877 at KLC1 203215 s at MYO6 89.8 209371 s at SH3BP2 203509 at SORL1 202964 s at RFX5 89.8 209371 s at SH3BP2 203509 at SORL1 214088 s at FUT3 89.8 209371 s at SH3BP2 203509 at SORL1 207131 x at GGT1 89.8 209371 s at SH3BP2 213198 at ACVR1B 211423 s at SC5DL 89.8 205490 x at GJB3 218995 s at EDN1 218542 at CEP55 89.8 205490 x at GJB3 218995 s at EDN1 205085 at ORC1 89.8 205490 x at GJB3 218995 s at EDN1 210092 at MAGOH 89.8 205490 x at GJB3 218995 s at EDN1 212570 at ENDOD1 89.8 205490 x at GJB3 218995 s at EDN1 203009 at BCAM 89.8 220658 s at ARNTL2 218080 x at FAF1 216468 s at ZNF682 89.8 220658 s at ARNTL2 210150 s at LAMA5 200604 s at PRKAR1A 89.8 200875 s at MIR1292 202046 s at ARHGAP35 216468 s at ZNF682 89.8 203068 at KLHL21 216533 at PCCA 211478 s at DPP4 89.8 203068 at KLHL21 216533 at PCCA 204753 s at HLF 89.8 203068 at KLHL21 218995 s at EDN1 208025 s at HMGA2 89.8 209125 at KRT6A 214772 at C11orf41 218995 s at EDN1 89.8 209125 at KRT6A 209049 s at ZMYND8 218020 s at ZFAND3 89.8 216805 at — 214772 at C11orf41 218995 s at EDN1 89.8 216805 at — 203785 s at DDX28 200764 s at CTNNA1 89.8

89 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 216805 at — 217698 at — 214033 at ABCC6 89.8 214772 at C11orf41 218995 s at EDN1 204128 s at RFC3 89.8 214772 at C11orf41 218995 s at EDN1 34449 at CASP2 89.8 214772 at C11orf41 205999 x at CYP3A4 207559 s at ZMYM3 89.8 205490 x at GJB3 37966 at PARVB 214772 at C11orf41 89.7 205490 x at GJB3 204128 s at RFC3 204124 at SLC34A2 89.7 205490 x at GJB3 218996 at TFPT 212078 s at MLL 89.7 205490 x at GJB3 212078 s at MLL 215945 s at TRIM2 89.7 209371 s at SH3BP2 204298 s at LOX 202580 x at FOXM1 88.2 211100 x at LILRA2 215603 x at GGT1 202580 x at FOXM1 88.2 209371 s at SH3BP2 217053 x at ETV1 88.1 217904 s at BACE1 211417 x at GGT1 86.8 217665 at ZNF813 211417 x at GGT1 86.8 201268 at NME1-NME2 218922 s at CERS4 86.8 201563 at SORD 218261 at AP1M2 86.8 211100 x at LILRA2 215603 x at GGT1 86.8 217904 s at BACE1 211417 x at GGT1 86.8 209371 s at SH3BP2 201236 s at BTG2 86.4 209125 at KRT6A 211373 s at PSEN2 86.4 214772 at C11orf41 218995 s at EDN1 86.4 215469 at — 211163 s at TNFRSF10C 86.4 221823 at C5orf30 65517 at AP1M2 86.4 208644 at PARP1 211685 s at NCALD 86.4 217904 s at BACE1 211417 x at GGT1 86.4 205490 x at GJB3 207125 at ZNF225 85.3 205490 x at GJB3 211751 at LOC653513 85.3 201250 s at SLC2A1 205229 s at COCH 85.3 205490 x at GJB3 207125 at ZNF225 85.3

90 SUPPLEMENTARY TABLE 10 — Continued

Probe Symbol Probe Symbol Probe Symbol Probe Symbol Probe Symbol Classiﬁcation 205490 x at GJB3 211751 at LOC653513 85.3 201250 s at SLC2A1 205229 s at COCH 85.3 201250 s at SLC2A1 205841 at JAK2 85.3