Supplementary Methods

Verhaak sub-classification

The Verhaak called tumor subtype was assigned as determined in the Verhaak et al. manuscript,

for those TCGA tumors that were included at the time. TCGA data for expression (Affymetrix platform, level 1) and methylation (Infinium platform level 3) were downloaded from the TCGA portal on 09/29/2011. Affymetrix data were processed using R and Biocondutor with a RMA algorithm using quantile normalization and custom CDF. Level 3 methylation data has already been processed and converted to a beta-value. The genes that make up the signature for each of the 4 Verhaak groups (i.e. Proneural, Neural, Mesenchymal, and Classical) were downloaded.

For each tumor, the averaged expression of the 4 genes signatures was calculated generating 4

‘metagene’ scores, one for each subtype, (Colman et al.2010) for every tumor. Then each subtype metagene score was z-score corrected to allow comparison among the 4 metagenes.

Finally, for each tumor the subtype with the highest metagene z-score among the four was used to assign subtype. Thus by this method, a tumor is assigned to the group to which it has the strongest expression signature. The shortcoming is that if a tumor has a ‘dual personality’ – for instance has strong expression of both classical and mesenchymal signature genes, there is some arbitrariness to the tumor’s assignment.

Western Blot Analysis and cell fractionation

Western blot analysis was performed using standard protocols. To determine protein expression we used the following antibodies: TAZ (Sigma and BD Biosciences), YAP (Santa Cruz

Biotechnology), CD44 (Cell Signaling), FN1 (BD Biosciences), TEAD1, TEAD2, TEAD3,

TEAD4 (Santa Cruz Biotechnology), MST1, p-MST1, MOB1, LATS1, LATS2, 14-3-3-,

1 ACTG2, (Cell Signaling), p-LATS1/2 (Abcam), Flag (Sigma Aldrich), Actin (Calbiochem),

CAV2 (BD Biosciences), CTGF (Santa Cruz), RUNX2 (Sigma Aldrich), Cylin A, Cyclin E,

Cyclin B1, p-cdk1, p-cdk4 (Cell Signaling Technologies). Protein extraction of GSCs was performed using 0.5% NP-40 lysis buffer containing 50 mM Tris-HCl (pH7.5), 150 mM NaCl,

50 mM NaF and supplemented with protease inhibitors (Roche) and PMSF just before use. For human glioma specimens, frozen tumors were dissected out and lysed with buffer containing 7M urea, 2M thiourea, 1% CHAPS, 50 mM Tris-HCl (pH 7.5). Protein concentrations were determined using the CB-X Protein Assay (G Biosciences). Nuclear and cytosolic fractionation was performed as previously described (Bhat et al.2004).

IHC

IHC analyses were performed on paraffin blocks, deparaffinized, and hydrated through an ethanol series. After microwave antigen retrieval, antibodies against TAZ (BD Biosciences or

Novus), FN1 (BD Biosciences), CD44 (BD Biosciences) or J1-31 (Millipore) were incubated with the slides overnight at 4 °C. Staining was performed using the DAKO Envision kit according to the manufacturer’s instructions (DAKO, Carpinteria, CA).

Methyl light assay

DNA was extracted from cell lines using a DNA isolation kit (Epicenter) and the protocol was followed per manufacturer. DNA was then bisulfite converted using a kit from Zymo per manufacturer instructions. Methylation status of TAZ was detected using a fluorescence based

Methyl Light PCR technique with COL2A1 as reference gene as previously described (Eads et al.1999, Eads et al.2000). Primers (F: TTATTACGTTTCGATTTCGGAAGTTCG and R:

CGCCCAAATAATACCCGCTAAAAC) and probe (CGCGCTCATCCGACACCACTCCAA)

2 were designed against the 2nd CpG island in the TAZ promoter using Primer Express software

(Applied Biosystems) against the amplicon; 5’-

GGGTAAGAGGAGACGGGTGTTTTTTATTTATTTTTTTCGGTCGCGCGGATTTTTTTCG

TTTAGATTTGTATTTGTATTTTTTTGAGTTTATTACGGATTTGGGGCGGGATT-3’.

Bisulfite sequencing

Genomic DNA was bisulfite converted as described above and the DNA was then inserted into a

Topo vector using the TopoTA Cloning for Sequencing kit (Invitrogen). Ten colonies were picked and plasmid DNA was isolated using a miniprep kit (Qiagen). Sequencing was done at the MDACC core facility and compared to the promoter sequence available on the

Transcriptional Regulatory Element Database website (http://rulai.cshl.edu/cgi- bin/TRED/tred.cgi?process=home) to identify methylated CpG’s.

RT-PCR mRNA was obtained using the QIAshredder kit (Qiagen) and the RNeasy Plus Mini Kit (Qiagen) followed by a two-step RT-PCR method. Briefly, 0.3–0.5 μg total RNA was reverse transcribed to generate first strand DNA (Invitrogen). To amplify the cDNA, Taqman primer probes in conjunction with 1× Taqman Universal PCR Master Mix (Applied Biosystems) were used for the following genes: WWTR1, ACTB1,CTGF, CD44, FN1, ADAMTS1, and IL8. RNase inhibitor

(0.4 units/μl; Roche) was included in every reaction. Reaction mixtures were incubated at 95 °C for 10 minutes for 1 cycle and then 15 s at 95 °C and 1 min at 60 °C for 40 cycles. The fluorescent signal was measured using the Applied Biosystems 7500, and the relative level of fold changes were calculated using the absolute Ct method. For the RCAS tumors, core

punches representing more than 90% of tumor tissue was used from paraffin embedded tissues.

3 Total cellular RNA was isolated form the core punches using the Epicentre RNA isolation kit according to the manufacturers protocol (Epicentre Biotechnologies, Madison, WI) following de- paraffinization and proteinase K treatment. Real time PCR was performed as above using mouse specific Taqman probes for CD44, FN1, CTGF and RPS3.

Small interfering RNA transfection

Transient knockdown was performed using siRNA constructs from Dharmacon against: scrambled control, TAZ, STAT3, C/EBP-, and CTGF.. Cells were transfected with siRNAs using Lipofectamine 2000 (Invitrogen) according to manufacturer recommendations. The final siRNA concentration was 60 nM and cells were collected and analyzed 72 h later.

Matrigel Invasion Assay

Cells were plated on transwells (ISC Bioexpress) coated with Matrigel (BD Biosciences) and allowed to invade through the matrigel overnight. Hema 3 staining kit (Thermo Fisher) was used to stain the cells that invaded through the Matrigel. The dye was extracted using 5% Sodium

Deoxycholate (Sigma) and an OD reading was done at 595 nm.

EdU labeling and flow cytometric analysis

Cells were chased with EdU for 2h followed by detection of S phase cells usingthe Click-iT EdU kit (Invitrogen A10202) per kit instructions.

Neurosphere Assay

Viability was calculated using the ViCell counter and 3 cells were plated per well in a 96-well flat bottom plate in triplicate. The number of wells containing neurospheres was counted three weeks after plating.

4 Immunoprecipitation

Protein G dynabeads (Invitrogen) were cross linked with primary antibody for 1 hour. Then cell

lysates were added to the beads and incubated overnight at +4°C. Beads were washed and

western analyses were performed to confirm interacting proteins.

Osteogenesis and chondrogenesis assays

Cells were seeded at a density of 5x104 cells in a 6-well plate. After 24 hours, cell differentiation was induced with Osteogenesis Induction Medium (Lonza). Cells were fed every 3-4 days by completely replacing the medium with fresh Osteogenesis Induction Medium. After 3-4 weeks, cells were rinsed in PBS, fixed with 70% ethanol and stained with Alizarin Red. For chondrogenic assay, cell pellets were prepared by spinning down 3x105 cells in 15 ml

polypropylene tubes and grown in Complete Chondrogenic Medium (Lonza). Cell pellets were fed every 2-3 days by completely replacing the medium with freshly prepared Complete

Chondrogenic Medium. After 3-4 weeks, pellets were fixed in buffered 10% formalin and embedded in paraffin. 5m sections were slide-mounted and stained for glycosaminoglycans with Safranin O.

NSC differentiation assays

To induce the differentiation of NSCs, neurospheres were exposed to Accutase for 5–10 minutes

and dissociated by triturating. Subsequently, the cells were plated in poly-d-lysine and laminin-

coated 12mm glass coverslips, at approximately 15-20,000 cells per well in neurobasal medium

supplemented with 5% FBS or without growth factors for 6 days at 5% CO2 and 37°C. At the

end of the differentiation period, cells were fixated with 4% PFA washed with PBS and

incubated in PBS containing 2% BSA and 10% NGS 1hr at room temperature to block

5 nonspecific antibody binding sites. Cells were then incubated with primary antibodies for 1 hr at

room temperature, or at 4°C overnight. After the washing step, cells were incubated with

appropriate secondary antibody for 1 hr at room temperature. To visualize nuclei, cells were

counterstained with Hoechst 3342 (Sigma). Coverslips were than mounted and examined under a

Zeiss fluorescent microscope.

Supplementary Figure Legends

Supplementary Figure S1. A. The MES subnetwork generated from the ARACNE analysis

displaying network map (n=231 genes). The nodes were then color coded to show the

membership of a given gene to a regulatory network. B. The expanded MES subnetwork

showing first neighbors from the initial subnetwork (n=906 genes). C. Dot plot of TAZ mRNA expression versus MES metagene score in TCGA GBM dataset (Affymetrix platform). Points are color coded as red or blue based on if the given tumor has a more MES or PN signature using composite

Phillips and Verhaak definitions. D. Cartoon depicting the HIPPO signaling pathway. Arrows

indicate activation, blunt heads indicate repression. E. CpG sites in the TAZ promoter 1000 bp

upstream of the transcription start site of TAZ is shown. Blue regions highlight CpG islands as

identified using Methprimer software (http://www.urogene.org/methprimer/index1.html). F.

Methylation status of HIPPO pathway gene promoters in 62 PN (blue) or 147 MES (red) GBMs

from TCGA dataset (Illumina Infinium platform). Black bar is the mean of the methylation beta-

score of either probe 1 (P1) or probe 2 (P2). Two-sample t-test between the groups was

performed to assess statistical significance. G. Methylation status of TAZ and YAP1 across the

four subtypes of GBM based on Verhaak called classification. Black bars in each column

represent the mean of the group. H. Methylation status of TAZ and YAP1 across the four

subtypes of GBM based on Verhaak calculated method. For each tumor, a metagene score was

6 calculated for the classical, MES, PN, and neural signatures. These scores were then z-score

corrected among all the tumors, and subtype was assigned based on the highest metagene for a

given tumor. See methods above for details of G and H. I. Western analysis of cell lysates from

frozen grade II-IV gliomas repositoried at MDACC. Cells were lysed using a special Urea buffer

(see Supp. Methods) and equal loading was assessed using actin antibody. J. IHC staining of

FN1 on grade II and grade IV gliomas. Note endothelial staining of FN1 in the grade II glioma

(left panel) compared to tumor cell staining in a grade IV glioma (right). K. IHC staining on 35

GBMs for TAZ and CD44. Tumors were classified as either negative, weakly positive (+) or

strong positive (++) for CD44 and negative, cytoplasmic or nuclear for TAZ. Representative IHC

images of negative staining left panel, or strong positive staining for CD44 (upper right) or

nuclear TAZ (lower right) is shown. Table below shows the staining patterns and Fisher’s exact

test p value. L. IF staining for TAZ and J1-31 in GBMs. TAZ expression is shown in green and

J1-31 is red. Merged image of both proteins is shown in two independent GBMs.

Supplementary Figure S2. A. Cell fractionation of GSCs and comparison of TAZ, and p-MST1

expression in nuclear versus cytosolic fractions. Lamin was used as nuclear fractionation control.

B. Kaplan-Meier analysis of patient survival in the TCGA datasets based on TAZ (left panel) or

YAP1 (right) expression. Log rank test was used to estimate statistical significance. NS=not significant. C. Representative IHC images (40x) of TAZ and CD44 in tumors in mice implanted with GSC20 non-targeting control (NT) or sh-TAZ-2 is shown.

Supplementary Figure S3. Western analysis of MES markers in GSCs 7-11 and 8-11 overexpressing vector or 4SA.

7 Supplementary Figure S4. A. Western blotting comparison of TAZ, and TEAD2-4 expression

in GSC20 and murine NSCs. B. Differentiation of TAZ overexpressing NSCs in basal media

without mitogens (bFGF and EGF). Top panel shows staining for FN1 (red), middle panel shows

SMA (green), and bottom panel shows MAP2 (red). Scale bars = 100µm.

Supplementary Figure S5. A. Western blotting of GSC20 transfected with siRNA against a

scrambled sequence (control), STAT3 C/EBP-or TAZ showing expression of respective

proteins. B. Western blotting of GSC11-4SA clone after stable transduction with siRNA against

CTGF. C. Heatmap of top 100 most induced genes in 4SA compared to vector as assayed by

Affymetrix HGU-133a3 microarray platform. Genes are ranked in order with the largest

magnitude of induction at the top. Calculated log2 expression values are shown for vector, 4SA, and 4SA-S51A. D. Real time q-PCR analyses of gene expression in GSC11 clones. The gene expression value of vector control was normalized to one and the relative expression of 4SA and

4SA-S51A is shown as bar graphs. t-test was used to calculate statistical significance. * denotes p value <0.005. E. Heatmap of 50 most suppressed genes in 4SA compared to vector, that return to baseline expression in 4SA-S51A, as assayed by Affymetrix HGU-133aa microarray platform.

Genes are ranked in order with the largest magnitude of suppression at the top. Calculated log2 expression values are shown for vector, 4SA, and 4SA-S51A. F. ChIP-qPCR of CTGF promoter occupancy by TAZ in 4SA versus S51A. Bar graphs represent percent of input occupancy by

TAZ. t-test was used to determine statistical significance.

8 Supplmentary Reference

Bhat KP, Itahana K, Jin A,Zhang Y. 2004. Essential role of ribosomal protein L11 in mediating growth inhibition‐induced p53 activation. EMBO J 23: 2402‐2412.

Colman H, Zhang L, Sulman EP, McDonald JM, Shooshtari NL, Rivera A, Popoff S, Nutt CL, Louis DN, Cairncross JG et al. 2010. A multigene predictor of outcome in glioblastoma. Neuro Oncol 12: 49‐57. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV,Laird PW. 2000. MethyLight: a high‐throughput assay to measure DNA methylation. Nucleic Acids Res 28: E32.

Eads CA, Danenberg KD, Kawakami K, Saltz LB, Danenberg PV,Laird PW. 1999. CpG island hypermethylation in human colorectal tumors is not associated with DNA methyltransferase overexpression. Cancer Res 59: 2302‐2306.

9 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1A

TAZ network C/EBP‐ network STAT3 network TAZ/C/EBP‐ overlap TAZ/STAT3 overlap C/EBP/STAT3 overlap TAZ/C/EBP‐/STAT3 overlap Hub (TAZ/C/EBP‐/STAT3) Not in networks

TAZ

C/EBP‐

STAT3

10 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1B

TAZ network C/EBP‐ network S3STAT3 network TAZ/C/EBP‐ overlap TAZ/STAT3 overlap C/EBP‐/STAT3 overlap TAZ///C/EBP‐/STAT3 overlap Hub (TAZ/C/EBP‐/STAT3) Not in networks

11 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1C

12 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1D

Cell-cell contact Other Extracellular Signals

Merlin Kibra

Rassf

14-3-3 Sav1 MST1/2

14-3-3 P YAP/TAZ MOB LATS 1/2

P Ajub YAP/TAZ

YAP/TAZ Cell Proliferation Cell Survival Anti-apoptosis TEAD1-4

13 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1E

14 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1F

p value: 0.80 0.40 0.009 0.04 0.76 0.54 0.09 0.18 0.20 0.62

P1 P2 P1 P2 P1 P2 P1 P2 LATS1 LATS2 MST1 TEAD1 TEAD2 TEAD4

15 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1G

Welch two sample t‐test

PN v/s CLASS p=0.0001 PN v/s MES p= 0.0001 PN v/s NEU p= 9.793e‐05

PN v/s CLASS p= 0.14 PN v/s MES p= 0.10 PN v/s NEU p= 0.06132

PN v/s CLASS p= 0.12 PN v/s MES p= 0.65 PN v/s NEU p= 0.81

N=55

16 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1H

Welch two sample t‐test

PN v/s CLASS p= 5.959e‐06 PN v/s MES p= 5.489e‐05 PN v/s NEU p= 0.0003

PN v/s CLASS p= 0.0046 PN v/s MES p= 0.27 PN v/s NEU p= 0.23

PN v/s CLASS p= 0.44 PN v/s MES p= 0.31 PN v/s NEU p= 0.13

N=279

17 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1I

Grade II/III Grade IV

1 23452 3 4 5 6786 7 8 123456781 2 3 4 5 6 7 8

YAP

TAZ

TEAD1

TEAD2

TEAD3

TEAD4

FN1

MST1

p-MST1/2

LATS1

LATS2

p-LATS1/2

14-3-3-

SMA

actin Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1J

Grade II Grade IV

FN1

19 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1K

GBM8 GBM32

CD44

TAZ

TAZ

negative/cyto nuc CD44 negative/single + 25 1 ++ 27

Fisher's exact test p < 0.0001

20 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS1L

GBM1 GBM2

TAZ J1‐31

21 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS2A

Nuclear Cytosol

Lamin p-MST1

TAZ Short expo.

TAZ Long expo.

22 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS2B

TAZ low YAP1 low TAZ high YAP1 high

23 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS2C

NT sh-TAZ-2

TAZ

CD44

24 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS3

7-11 8-11

FN1 CTGF TAZ actin

25 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS4A

TAZ actin

TEAD2 actin

TEAD3 actin

TEAD4

actin

26 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS4B

vector TAZ 4SA 4SA-S51A nectin o Fibr A SM map2

27 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5A

siRNA

STAT3

50 kDa

37 kDa C/EBP-

25 kDa

TAZ

actin

28 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5B

GSC11-4SA

CTGF

Cav2

CD44

actin

29 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5C

30 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5D

ADAMTS1 CD44 30

n 10 * 9 25 8 * 20 7 6 15 5 4 10 3

Relative expressio 2 5 1 0 0 Relative expression

CTGF IL8 60000 900 * 800 * 50000 700 40000 600 500 30000 400 20000

300 Relative expression lative expression 10000 e 200 R 100 0 0

FN1 7 6 * 5 4

expression 3 2 1 Relative 0

31 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5E

32 Bhat, Salazar, Balasubramaniyan et al _Supp. FigS5F

CTGF 6

4

2 % input

p <0.001

0

33 Supp Table S1A: List of TFs used in this study versus Carro et al. 2010

Common TFs Carro et al. unique Bhat et al. unique NFYA AEBP1 SCMH1 HOXA11 AFF3 ZBTB32 MEOX1 AHCTF1 DPEP1 CREBBP ATBF1 WWTR1 C2orf3 ATF4 HOXC8 ZNF263 BAPX1 MED17 DLX6 BCL6 FOXN3 ETV1 BHLHB2 FOXC1 GTF2IRD1 BHLHB3 GSC2 GAS7 BRPF1 TAF2 PAX6 CEBPA POU1F1 TEAD3 CEBPD TAF11 E2F2 CEBPZ HLTF TFAP2B CHES1 TP63 NFIX CIR ZNF37A PAX7 CREBL1 GTF3C1 MLXIPL CSDA GTF2I BAZ1B CTBP1 UBE2K ETV7 CTBP2 AKR1B1 ZNF207 CUTL1 RRN3 NR1H4 CUTL2 KCNH4 SLC30A9 DAXX POU4F3 ISL1 DENND4A GMEB2 SNAI2 DLX4 ADNP2 HSF2 DR1 HTATSF1 NR1H3 DSCR1 TAF7L POU2F2 DUX1 TAF1C ARNTL2 E2F6 GABPB1 NR2E3 ERCC6 BRF2 ARID4A ESRRB RNASEH2A BARX2 ETV5 ETV2 SCML1 EVI1 GARS FOXP3 FALZ PDLIM1 NFE2L3 FEZF2 UBTF ALX4 FMNL2 ACCN1 PRDM1 FOXG1B HNF1B MXD1 FOXO1A NKX3‐2 LZTS1 FOXO3A HTATIP2 RNF4 FOXP1 PDHX RFXANK FUBP3 PRDM4 HMG20B GABPB2 CYP27B1 FOXJ2 GMEB1 MYF5 NFYC GRLF1 CUX2 SPI1 HBP1 HCFC2

34 CBFB HES1 BTN3A3 MEF2A HES2 SIM1 TFE3 HIF3A MED23 PITX1 HIVEP1 TBP RORA HIVEP2 SUB1 MNT HIVEP3 TCERG1 TCF3 HKR3 GTF3C2 SREBF1 HLX1 HDAC1 AFF4 HLXB9 ASH1L NFATC3 HMGA2 IVNS1ABP TBX21 HMGB1 PROX1 GLI2 HOP CD3EAP ENO1 HOXA10 FOXO3 FOSL2 HOXA4 ELL2 RARB HOXA5 GTF3C3 NFKB2 HOXA6 ONECUT2 MLLT10 HOXA9 HOXB3 CBFA2T2 HOXC4 HOXB1 TP73 HOXC5 KCNJ5 RUNX1T1 HOXC6 TAF12 SP140 HOXD4 ETF1 RFX3 H‐plk ZSCAN18 TCF7 HTLF GTF3A MEF2C IKZF1 HOXC13 PGR IKZF5 BATF3 NFE2L1 INSM1 RBPJL ZNF446 IPF1 C11orf9 MYNN IRF4 GTF3C4 NFX1 IRF6 GTF2F1 TFAP2C ISGF3G NR1D1 LHX5 JARID1A PKMYT1 TBX5 JARID1B CSRP3 ZBTB25 KIAA0415 MLLT1 TFAP4 KIAA0963 MNX1 LASS4 KLF6 TAF4 SLC26A3 KNTC1 NPAS1 ZFHX4 L3MBTL BARX1 ESR1 LASS6 ZSCAN5A CEBPE LOC645682 LHX1 BTAF1 LYL1 HSD17B4 CREM LZTFL1 MED6 MZF1 MAML3 EIF2S1 LZTR1 MDS1 HNF1A HIRA MECP2 EHF SOX10 MEF2B NKX2‐1 XBP1 MEIS3P1 BRIP1 EP300 MIZF HLX

35 HIF1A MLL4 DMRT1 YY1 MLLT7 KIAA0319 NFATC4 MLXIP GCM1 VSX1 MSL3L1 CREBZF MYBL2 MYB YAP1 HNF4A MYBL1 GTF2B ADNP MYST2 ALS2CR8 TCFL5 NANOG LEF1 E2F1 NCOR1 PDX1 SMAD7 NHLH1 GTF2A2 ELF4 NHLH2 ZFHX3 SCML2 NKRF NOL3 GATA1 NPAS3 TAF4B KLF5 NPAT TAF1A TSC22D1 NRF1 TMF1 HSF4 PAX1 GC NFAT5 PAX2 BTF3 CTCF PAX9 ABT1 ZNF500 PBX2 ZNF41 FOXF1 PCGF2 TAF1 SOLH PEG3 SLC25A37 ZNF174 PHF2 GTF3C5 SALL1 PHTF2 ZEB1 MAZ PLAGL1 ANKRD1 TRPS1 PML TAF5 RELB PPARG FOXO1 SNAPC2 PREB TIAL1 CRX RBL2 MED21 ZNF175 RBPSUH SMARCA5 DBP RBPSUHL GTF2E1 KLF1 REST MIA3 USF2 RFX2 GABPA ERF RREB1 MED7 ZNF85 RUNX3 ALX3 SP4 SHOX ZSCAN12 DLX5 SMARCA3 RCAN1 TFEC SNAI1 AIRE HOXA1 SNFT PMF1 HOXA2 SOX11 CUX1 HOXA3 SOX17 IKZF3 EVX1 SOX3 TAF6L BUD31 SP3 MFI2 ZKSCAN1 TADA2L PITX2 PAX4 TADA3L TLX3 MEOX2 TAL1 GTF2A1 POU6F2 TCF1 GFI1B AHR TCF2 TAF10

36 GLI3 TCF21 MLL2 LHX2 TCF8 SF1 LHX6 TGIF RBPJ CREB3 TNRC4 GDNF LHX3 TP73L SOX14 EDF1 TRERF1 ZEB2 GATA3 TWIST1 ZFPM2 TLX1 YBX1 PA2G4 PITX3 YWHAE SCRT1 TFAM YWHAZ FOXN2 AATF YY2 HOPX HOXB6 ZBTB16 TCEA2 MLX ZBTB22 UTF1 HLF ZBTB43 ZNF80 FOXN1 ZBTB6 ASCL3 SUPT6H ZBTB7A FOXG1 PHOX2B ZF ZSCAN2 NFKB1 ZFHX1B FOXC2 ELF2 ZFP37 TGIF1 KLF3 ZFP95 TAF7 CBL ZFX MGAM MYF6 ZFY ALX1 ELK3 ZIM2 FOXO4 FOXM1 ZMYM2 SRY CREBL2 ZMYM3 L3MBTL1 VDR ZMYM4 FOXD2 PPARD ZNF10 TAF9B BACH2 ZNF12 ZKSCAN4 E2F3 ZNF124 GTF2F2 NR2E1 ZNF137 LITAF TFEB ZNF14 ZKSCAN3 SRF ZNF141 SUPT3H BRD8 ZNF146 HDAC2 PFDN1 ZNF155 ZKSCAN5 HAND1 ZNF16 ZSCAN16 IRX4 ZNF160 GTF2E2 NR3C1 ZNF177 ZNF165 SMAD5 ZNF180 HNRNPAB CDX1 ZNF184 TAF13 TFDP2 ZNF185 NCOA6 TFCP2L1 ZNF187 ZBTB48 TLX2 ZNF195 GTF2H4 STAT1 ZNF20 IRF9 ZNF142 ZNF200 EBF2 TAF1B ZNF204 PSG1 DLX2 ZNF205 ATF2 ZNF212

37 EPAS1 ZNF22 ARID3A ZNF221 VAX2 ZNF222 NFE2L2 ZNF223 PRRX1 ZNF224 MEF2D ZNF225 PRDM2 ZNF226 PHTF1 ZNF227 ZBTB17 ZNF228 NR5A2 ZNF230 MYCL1 ZNF235 RLF ZNF239 ETV3 ZNF248 BLZF1 ZNF250 MLL ZNF253 ATF6 ZNF259 CREB1 ZNF26 KLF7 ZNF264 TGIF2 ZNF266 UBN1 ZNF267 KLF12 ZNF268 SATB2 ZNF271 KLF9 ZNF273 NR4A3 ZNF278 HOXB8 ZNF282 HOXB5 ZNF286 HOXB7 ZNF289 MSX2 ZNF291 ELF1 ZNF292 SMAD9 ZNF294 EGR1 ZNF302 NR2C1 ZNF304 NFYB ZNF306 TARDBP ZNF307 TRIM25 ZNF313 TBX2 ZNF318 TBX4 ZNF32 ZNF211 ZNF322B MYOG ZNF324 HOXA7 ZNF329 NEUROG3 ZNF330 EGR2 ZNF331 ATF1 ZNF334 NR4A1 ZNF335 HOXC11 ZNF337 NFE2 ZNF34 IKZF4 ZNF343

38 ZNF45 ZNF345 SPDEF ZNF350 SOX4 ZNF358 DEK ZNF364 RUNX2 ZNF365 SOX21 ZNF384 IRF1 ZNF394 SOX9 ZNF395 SLC2A4RG ZNF403 PAX8 ZNF407 FOSB ZNF408 FOXA2 ZNF409 NKX2‐2 ZNF410 ZNF133 ZNF415 TCF15 ZNF419A CITED1 ZNF42 MAX ZNF423 PLAGL2 ZNF426 THRA ZNF43 IRF3 ZNF430 STAT5A ZNF432 ELK1 ZNF435 SIX1 ZNF44 YEATS4 ZNF440 KLF2 ZNF443 SMARCA4 ZNF447 IRF5 ZNF451 HOXD1 ZNF460 HOXD3 ZNF467 HOXD9 ZNF468 HOXD10 ZNF471 HOXD11 ZNF473 HOXD13 ZNF480 MYOD1 ZNF484 E2F8 ZNF493 SOX15 ZNF506 FOXA1 ZNF507 NRL ZNF508 FOXJ1 ZNF510 CBFA2T3 ZNF516 TULP4 ZNF518 JUND ZNF528 TRIM28 ZNF529 ZNF236 ZNF532 NFATC1 ZNF536 CDX4 ZNF544 NR1H2 ZNF549

39 RARA ZNF550 ZNF132 ZNF551 NR0B2 ZNF552 RFX1 ZNF556 TRIM22 ZNF557 RFXAP ZNF562 E2F5 ZNF573 ARNTL ZNF574 MEIS2 ZNF576 NOTCH2 ZNF580 MYCN ZNF586 RAX ZNF587 SOX5 ZNF588 CLOCK ZNF589 ETS1 ZNF592 TBX3 ZNF593 DMTF1 ZNF606 ELF5 ZNF609 TFCP2 ZNF611 HEY2 ZNF614 EGR4 ZNF623 EMX1 ZNF629 TAF5L ZNF638 PAX3 ZNF643 NKX2‐8 ZNF646 VEZF1 ZNF652 TBR1 ZNF654 GATA4 ZNF659 KLF4 ZNF665 ZNF189 ZNF667 NR5A1 ZNF668 LMX1B ZNF669 MYC ZNF671 ZNF193 ZNF672 TFAP2A ZNF673 FOXF2 ZNF675 HMGA1 ZNF682 TRIM29 ZNF688 POU2F3 ZNF692 SMAD6 ZNF695 SIX3 ZNF696 LBX1 ZNF7 STAT4 ZNF701 ETV6 ZNF702 ASCL1 ZNF706 RB1 ZNF710 ESR2 ZNF711

40 TCF12 ZNF74 HMG20A ZNF75 IRF8 ZNF79 ZNF434 ZNF8 TCF25 ZNF84 ZNF287 ZNF91 GATA6 ZNF93 TP53 ZNF96 FOXK2 ZNFN1A1 MBD1 ZSCAN5 SMAD4 NFIC VAV1 SPIB RERE PRDM16 LMO4 CREG1 RXRG TBX19 POU2F1 NR1I3 RORC RFX5 LASS2 ARNT ILF2 SOX13 MEIS1 NR1I2 CREB5 HMBOX1 ST18 NFIB NR6A1 REXO4 MSRB2 TCF7L2 ZNF215 MTA2 TBX6 CCRN4L THRB POU4F2 NR3C2 VENTX FLI1

41 POU4F1 TCF7L1 ZFP36L2 HHEX ZNF117 ZIC1 NR4A2 UBP1 CEBPG KLF10 CNOT8 BATF BACH1 GATAD1 TSC22D3 ERG ETS2 CREB3L1 ELK4 HOXB13 RUNX1 SIM2 NR2F6 PKNOX1 ZBTB7B FOXH1 FUBP1 ZNF281 ATF3 REL NEUROD1 EN1 MSX1 VPS72 ELF3 FEV NKX6‐1 HESX1 ZNF148 KLF15 HEYL HMGB2 HAND2 CITED2 T PTTG1 HEY1

42 HNF4G EN2 NFIL3 PHOX2A PKNOX2 CDX2 SNAPC4 ZNF219 SALL2 ZNF202 LMO1 ZNF143 ZNF3 STAT6 TSC22D4 SMAD3 NKX3‐1 TEF PBX3 PRRX2 SP2 GATAD2A ZNF444 ZNF83 TBX10 ZNF232 E4F1 CTNNB1 FOXI1 IRF2 HR GBX2 STAT3 SHOX2 AR ZNF354A ATF5 NR0B1 BNC1 CNBP ONECUT1 KLF13 ZNF35 HOXD12 NFRKB FOS SMAD1

43 EMX2 NPAS2 SIX2 STAT2 ATF7 HOXB9 SCAND1 JUNB NEUROD2 ZNF274 ZNF217 FOXB1 KLF11 CEBPB ATOH1 ZNF131 ARNT2 TCEAL1 ZNF24 AFF1 HCFC1 OVOL1 RARG RELA ESRRA STAT5B HOXB2 MGA ZHX3 SNAPC5 NR1D2 DDIT3 PROP1 SMAD2 DRAP1 FOSL1 NR2F1 ETV4 ZNF135 FOXL1 SCAND2 IRX5 SIX5 ZBTB38 HIC1 NR2C2 JUN

44 SOX12 MAF ZHX2 MSC FOXE1 GATA2 EGR3 ZNF238 CIITA ZNF154 HCLS1 HOXC10 SOX2 PLAG1 NEUROG1 CREB3L2 SATB1 EWSR1 SOX1 MTA1 NKX2‐5 TFDP3 ASCL2 FOXD1 TBX1 POU6F1 SIX6 POU3F2 WT1 MAFF BRF1 HSF1 PURA IRF7 NR2F2 SP1 PBX1 ZFP36L1 POU3F1 RXRA ZNF197 MYT1L FOXE3 PPARA TEAD1 MITF FOXD3

45 MTF1 MYT1 ZNF167 ZNF140 TSC22D2 ESRRG TCF4 ZNF136 ZNF33B POU3F4 MAFG ZNF81 TEAD4 TFDP1 ZNF192 MAFK CNOT7 FOXJ3 ZNF277 SREBF2 POU3F3 RORB SOX18 MAFB RXRB E2F4 OLIG2 SUPT4H1 ZNF134 HMX1 ZNF323

46 Supp Table S1B: List of genes used in signature classification by Phillips et al. 2006, and Verhaak et al. 2010

Verhaak.MES Verhaak.PN Phillips.MES Phillips.PN Verhaak.Classical Verhaak.Neural Phillips.Proliferative LOX GPR17 LIF CDR1 EGFR AGXT2L1 CHAF1B FHL2 TMSL8 PI3 FSTL5 MEOX2 CCK TTC12 COL1A1 KLRC3 SPOCD1 psiTPTE22 SOCS2 CRYM E2F7 COL1A2 DCX IL32 CSDC2 NOS2A MYBPC1 C4orf47 FCGR2B PCDH11Y ANGPTL4 KLRC3 CDH4 NTSR2 NDC80 AIM1 KLRC4 HK3 ZNF488 ELOVL2 GRM3 NUF2 IGFBP6 NR0B1 SBNO2 SUSD5 KCNF1 HPCAL4 CENPN DCBLD2 HRASLS TAGLN LOC650392 PDGFA TMEM144 RPA3 SERPINE1 RAB33A SERPINE1 DLL3 CENTD3 GPR22 CENPK SRPX2 ERBB3 FCGR2C FERMT1 GRIK1 SERPINI1 ARNTL2 LY96 RP11‐35N6.1 MYL9 GALNT13 CAMK2B PPP1R1A NEK2 PLAU C20orf42 NRP1 NCAM1 ACSBG1 KCNK1 IL13RA2 CLEC2B CA10 COL4A2 EPHB1 GAS1 VSX1 PLK4 CSTA MYT1 PDPN JPH3 VAV3 SH3GL2 CCNE2 BNC2 SOX10 COL4A1 DOK6 RGS6 HPCA NCAPG THBS1 EPHB1 LOC100132244 SSTR1 KLHL4 GABRB2 HMMR FPRL2 GRID2 TIMP1 STOX1 MEIS1 DHRS9 ASPM MS4A4A KLRK1 CHI3L1 RASL10A SLC4A4 DYNC1I1 IFT74 RAB27A DLL3 PLA2G5 SNAP91 MYO5C FXYD1 ANKRD5 TGFBI SOX4 PDLIM4 CNTN3 FGFR3 CPNE6 WDHD1 COL5A1 DNM3 NRP2 NDRG2 KLHDC8A SLCO1A2 CDKN2A DSE PAK3 EHD2 SOX8 HS3ST3B1 VIP DTL PLAUR SLC1A1 FOSL2 SCD DENND2A FEZF2 RBM24 FLJ22662 GPR23 BCL3 LOC254559 FLJ21963 ADD3 TOP2A THBD SCN3A RYR3 SMOC1 MAB21L1 CLCA4 MLF1IP IL1R1 CHD7 UNC93B1 FLJ16779 ZFHX4 LOC201229 RAD51AP1 ARPC1B AMOTL2 SERPINA1 GFRA1 EYA2 GRM1 MELK P4HA2 SATB1 ICAM1 CSMD3 TRIB2 EDG1 TYMS NCF2 CLGN FBN1 ATP6V1G2 NES EVI2A CRNDE LAMB1 PCDH11X FES ENHO B3GALT1 CAMK2G GINS1 MVP CNTN1 SOCS3 GABBR1 SHOX2 NDRG2 RRM2

47 PSCDBP TMEFF1 S100A11 SCG3 CREB5 ANKRD46 KIAA0101 IFI30 TOX3 HSD3B7 NTRK2 WSCD1 CHN1 SHOX2 COL8A2 NOL4 SERPINH1 GABBR2 RASGRP1 KCNJ3 GINS2 CNN2 FAM77C RAB34 LRRC4 FZD3 CA4 ECT2 TIMP1 LRRTM4 ACTN1 RUNDC3A IRS2 CRYL1 HSPB11 MAFB WASF1 C22orf26 TMEM100 SPRY2 PPP2R5A ZNF367 SLAMF8 DGKI METTL7B SMAD9 SOX9 TSNAX C6orf173 FER1L3 NKX2‐2 ANGPT2 SPHKAP CDH6 FUT9 FANCI ADAM12 C6orf134 FAM20C ZDHHC22 ACSL3 ANXA3 MAD2L1 C5AR1 GNG4 PMEPA1 FAM13C SEMA6D ACYP2 EMP2 NRP1 ZNF804A ANPEP DPP10 LFNG SLC30A10 PDK1 LAIR1 PAK7 RUNX1 PCSK6 ITGA7 CASQ1 EZH2 S100A11 PDE10A GGN REPS2 SLC6A11 FLJ22655 ERCC6L TNFAIP8 IL1RAPL1 SLC39A8 SLC25A21 ADAM19 NSL1 TTK CTSC SOX11 LZTS1 NKAIN4 ABCD2 MBP CCNB1 C1orf38 C1orf106 EMP3 LUZP2 TLE2 SLC31A2 HAUS1 SQRDL CRMP1 MYH9 GAD1 MLC1 SEPP1 FBXO11 LY75 CXXC4 LRRC32 SNRPN MEGF8 IMPA1 CKS2 DAB2 C1QL1 CA12 PDE2A BLM ZNF323 CENPI MAN2A1 MLLT11 LRRC29 GRID1 QTRT1 YPEL5 ABCA5 CTSB P2RX7 TNFRSF10D SGCG LMO2 SEPW1 C1orf97 ITGA5 STMN4 PLEKHF1 GNAL CDK6 UROS KIF23 LTBP2 KIF21B ACTA2 OLIG2 LRRC16 MRPL49 XRCC4 FCGR2A OLIG2 NEURL2 ALDH5A1 TGIF2 CRBN MCM2 MAN1A1 GRIA2 PLAUR KCTD4 ZNF211 THTPA DBF4 MSR1 MCM10 DLC1 TIMP4 LHFP TTPA CCDC138 STAB1 DUSP26 SHC1 OPCML CD97 FBXO3 DHFR LTBP1 FLRT1 ITGA7 ACSM5 PIPOX LYRM1 HJURP SAT1 ALCAM SLC25A37 SH3GL2 SIPA1L1 SH3GL3 DSN1 TES PLCB4 PAPPA C1QL1 ZNF264 RND1 KIF14 ITGA4 FGF9 FLNA WDR86 GNG7 MAT2B EXOSC9 TNFAIP3 CRB1 HOMER3 JPH4 ITGB8 MGST3 FBXO5 S100A4 LPHN3 THBD BCAN ZNF228 CRYZL1 TRMT6 TCIRG1 STMN1 C1RL DLL1 PLA2G5 GUK1 SMC4

48 LCP1 FHOD3 LPAR1 FAM133A ZNF419 SNCG NPHP1 IL4R KIAA1166 PLAU TNKS2 CDH2 ENPP2 DLGAP5 CDCP1 HN1 SLC22A18 FGF14 EXTL3 CCDC121 CHEK1 CASP4 SORCS3 PARP10 CALN1 ZNF227 AKR7A3 GGH PTPRC PHF16 SLC16A3 NRG3 FBXO17 TCEAL1 CCNA2 CD14 YPEL1 VWA1 ARPP‐21 ZNF134 EDIL3 YEATS4 LAPTM5 MMP16 LOC255783 RAC3 LAMB2 GABARAPL2 MDFIC CD4 LRP6 OSMR THRA AKT2 COX5B SLC25A24 SHC1 LOC81691 BHLHE40 RIPPLY2 SEMA6A PDE6D CDC2 PLS3 CDC7 TNC MPPE1 CLIP2 KIAA1598 NUSAP1 TLR2 RAP2A MMP14 KIF21B CENTD1 MDH1 DONSON ARSJ BCL7A TWF1 OVOL1 NR2E1 ORC4L ZWILCH NCF4 ZNF711 C1QTNF1 USH1C JAG1 SCHIP1 TIFA LCP2 MARCKSL1 PVRL2 SEC31B MGC2752 CALM2 SGOL2 PSCD4 FAM125B NCLN MCF2 PTPRA PEX19 ITGA2 ACSL1 MTSS1 CD151 SHD ZNF606 ATP5F1 MND1 ITGB2 TTC3 PTRF NEU4 PCSK5 USP33 HAUS6 ECGF1 CLASP2 PDLIM7 ZNF804A ZNF45 ATP5L PCNA FOLR2 HDAC2 ITGA3 C13orf15 SLC12A4 SNX11 CDC6 FXYD5 VAX2 C1R DSCAML1 ZNF671 MAGEH1 CENPA SERPINA1 CASK FLT1 BMP2 PTPN14 TTC1 TOM1L1 GNA15 TMEM35 TTC38 MAPT MCC ANXA7 NCAPH GCNT1 ZNF643 SHROOM3 GLUD1 ZNF20 BCAS1 CHAF1A NPC2 GADD45G CD97 FGF12 GPR56 NDUFS3 CENPE MYH9 MAP2 DEF6 KCNQ5 CALM1 ARRB1 WDR34 PDPN REEP1 JUNB GRIA1 HSPBP1 PEX11B MCM6 CASP1 ZNF286A FGG NALCN GLG1 CDC42 C1orf133 ST14 ZNF248 IFITM2 KCNN3 PRKD2 HPRT1 PAWR SLC16A3 PFN2 TRIM47 SLITRK5 PEPD ANKS1B CACYBP RAC2 MYB LOC151300 CALCRL ARNTL ROGDI KIAA0895 CAST FAM110B SLC12A9 NRSN1 TMEM161A PPFIA2 KNTC1 BDKRB2 CDK5R1 FGFRL1 ABLIM3 DMWD PRPSAP2 ACYP1 TGFBR2 SEZ6L BACE2 LGR5 GNAS UGT8 AURKA LGALS3 TAF5 FAM38A DUSP26 NPAS3 ATRNL1 CENPF

49 WWTR1 GSTA4 ITGA5 NET1 DLC1 MMD BRCA1 SIGLEC9 TMEM118 ESM1 GLUD2 CD151 PLCL1 ITGB3BP PTRF DBN1 SGSH PHYHIPL LRP5 SIRT5 RAD51 ARHGAP29 PODXL2 TPP1 PLCB1 TGFB3 REPS2 CDCA7 TRIM38 NRXN1 OSBPL3 ALDOC ZNF8 FAM49B TRIM36 PTPN22 HOXD3 EMP1 CRYAB RFXANK MGC72080 TMEM106C CTSZ SEC61A2 EFEMP2 CMTM5 JUND POPDC3 KIF18A FLJ20273 AOF2 CD248 LOC153811 PRPF31 ENPP4 GCLM RBMS1 NCAM1 RRBP1 FGF13 VPS16 CUTC TMEM79 CCR5 RBPJ PDGFA FUT9 RBCK1 MSRB2 ZC3HAV1L HEXB MMP15 MAP2K3 APOE GRIK5 TPM3 TMEM38B CD2AP ATAD5 EPAS1 PRKCZ ZNF235 SGK3 KIF4A SLC11A1 CSNK1E HRH1 GABRA3 TBX2 TCEAL2 E2F8 MYO1F ASCL1 MVP PKNOX2 GJA1 BEST1 ANKRD32 FNDC3B ZEB2 C15orf52 GRIA2 SEPT11. PPA1 ORC6L ANXA2 HMGB3 STEAP3 OLIG1 TMEM147 PGBD5 SIP1 SLC10A3 TOP2B FPR2 KCNB1 IRF3 CDR1 HELLS PYGL PELI1 CECR2 ID4 POMT2 ACSL4 RBBP8 LILRB2 ATP1A3 EFNB2 ELMO1 SLC6A9 FHIT PPIC NOD2 ICK GPR116 MAF DAG1 SPAST RFC4 LILRB3 TMCC1 ZYX CNTN1 ERCC2 MORF4L2 SPIN4 ALOX5 PPM1E IFITM3 NTN4 RBM42 AGTPBP1 PABPC4L RUNX2 TNRC4 ECE1 GABRB3 POFUT1 NANOS1 HMGB2 TNFRSF1B E2F3 KLF16 RP11‐35N6.1 NPEPL1 BASP1 C12orf48 ITGAM SCG3 SALL4 P2RX7 SARS2 PARP8 RRM1 IQGAP1 DPF1 TRABD GRIA4 ZNF304 SAR1A PRPS2 UAP1 EPB41 PDGFRL RASGEF1C TMED1 GNAI1 LSM5 KYNU TOPBP1 RHOJ CECR6 LRFN3 EPB41L3 MAGOHB RAB32 BCOR TRIM56 PTGDS ZNF446 PSCD1 MTF2 PROCR BEX1 RRAS HLF RGS12 SLC16A7 EFCAB2 TNFRSF11A SPTBN2 RTN1 BTBD2 DEK SFT2D2 ARHGEF9 HSPA12A RIN1 C3orf14 PTGER4 CAMSAP1L1 ADCY2 FZD7 NUCB2 COPZ2 PAFAH1B3 PDK4 GLI2 BARD1

50 ACPP DPYSL4 SGSM1 SMO USP1 CLIC1 NCALD ASCL1 ANXA5 TTC26 RRAS ZNF184 PHACTR3 KEAP1 LMNB1 IL15RA PPM1D FRY OSBPL3 TCF19 MAN2B1 BCAN HS3ST4 RFX2 RECQL ICAM3 PURG RAB11FIP4 SCAMP4 GJC1 AMPD3 RALGPS2 CYFIP2 CD3EAP TMEM14B ANXA1 SLCO5A1 PSD SNTA1 ABHD3 DSC2 FBXO21 PID1 C19orf22 BUB1 SH2B3 GSK3B KSR2 EPHB4 C3orf34 FMNL1 CBX1 RPRM KLHL25 GMPS CHI3L1 RALGPS1 DSCAM DOCK6 MLF1 POLD4 RUFY3 FLRT1 CC2D1A CCDC34 SCPEP1 CDC25A SLIT1 APBA3 MNS1 PTPN6 MARCKS ZC3H12B NDP STIL ELF4 GABRA3 DNM3 FLJ11286 EVC2 CEBPB MPPED2 SEZ6L KIAA0355 SHFM1 DRAM NRXN2 CRTC1 TRIP6 ZWINT WIPF1 ABAT AP2B1 HMG20B CEP152 VDR MAPT ZCCHC24 TEAD3 C1orf112 MFSD1 FXYD6 SLITRK2 GALNT4 PPIG HEXA LOC55565 P2RY13 NR2F6 CDC25C MAPK13 MAST1 FBXO2 SLC2A10 SPC24 HK3 RAD21 FAM19A5 M6PRBP1 NASP SEC24D VEZF1 C11orf2 SSH3 E2F1 STAT6 ZNF510 HIP1R LRP10 CDK2 ANXA4 CDKN1B F2 PMP22 C17orf75 CASP5 PHLPP CCNK GSTK1 SMC2 STXBP2 ACTR1A PLEKHB1 ILK ACN9 GRN NLGN3 GGTA1 CENPL LGALS1 WDR68 NOG WEE1 MGAT1 CSPG5 HEY2 PPIL5 FHOD1 MYST2 SCN3A C3orf15 DOK3 BAI3 FBXL15 LRIG3

51 RAB11FIP1 MATR3 TMOD2 MAGOH MRC2 SRGAP3 FXYD6 ATG12 LHFPL2 SNX26 SLC1A4 CREBZF CLCF1 GPM6A B3GAT1 PEG10 PLK3 SOX2 ABLIM1 EIF1AX LYPLA3 C1orf61 SORBS1 TIMELESS TMBIM1 MYO10 TPCN2 PIN4 VAMP5 TSPAN3 TPM1 TEX9 RHOG CKB IL17D FANCD2 FURIN TTYH1 TMEM59L PRIM2 TGOLN2 DPP6 MMP16 CDKN2C ENG 8‐Mar PAIP1 RABGAP1L EFHA2 TMPO PGCP FSD1 ASL EHD3 LRRFIP1 SORCS3 EMP3 ABHD6 ZNF217 DNAJC12 C1orf54 KIF5A GLT25D1 GRIK4 SYNGR2 SOX6 EFEMP2 RPL13 ALDH3B1 FAIM2 FES OMG TEC DTX4 TNFRSF1A PKP4 TRPM2 EPB41L2 CASP8 RPL37 TLR4 C12orf53 SIGLEC7 GAB2 SWAP70 TMLHE EHD2 KIF1A BATF BEND7 SP100 AJAP1

52 CCDC109B GPR158 UCP2 WNT7B RELB TRIM31 SYPL1 RASSF4 MGST2 PARD3 TRIM22 GNAO1 BLVRB SLC1A1 TRADD ATRNL1 HFE NUMA1 RBKS PCSK1N CYBRD1 TTYH1 PIGP TAL1 PHF11 GPRC5B S100A13 HDAC5 YAP1 ARL3 SSTR2 NAP1L3 LOC284244 MN1 C20orf19 RIMS2 ARHGAP22 LOC202451 AKR1C1 ANKS1B FAM110B ASB13 MAPK8IP2 PDK2 SE FAM155A RGS9 PAR5 CBX7

53 IKZF5

54 Supp Table S1C: Candidate TFs/co‐factors identified by ARACNE as associated with the MES network

Column1 Hub Spearman corrleation a/r 2 CEBPB 0.510496228 activator 3 ELF4 0.43196481 activator 4 MAFB 0.431430639 activator 5 HCLS1 0.423423212 activator 6 FOSL2 0.421634615 activator 7 TAZ 0.399745193 activator 8 ZNF217 0.36304453 activator 9 LASS2 0.357428575 activator 10 TRIM22 0.320569225 activator 11 YAP1 0.31862866 activator 12 STAT3 0.27949123 activator 13 LZTS1 0.260116533 activator 14 MYT1L ‐0.238588745 repressor 15 THRA ‐0.31230566 repressor 16 ZNF238 ‐0.38806662 repressor 17 ASCL1 ‐0.431996926 repressor

indicates TFs already identified by Carro et al. 2010 indicates co-factors novel to our study indicates TFs included in the master list of TFs by Carro et al. 2010

55 Supp Table S1D: Genes identified by ARACNE as associated with a TF network

TAZ network C/EBP‐network STAT3 network TPD52L2 MAFF DDX41 INHBB CYP1B1 ANKRD46 THADA C5AR1 PMP2 DAPK2 CAST PCSK2 TNFRSF10B TFE3 VIM NDRG3 NUPR1 CD93 C5AR1 KIT ENSG00000236772 PCSK2 CALHM2 SNTB1 CAST RHOG NID1 GBP1 EMILIN1 SLC3A2 MAPK11 ARMCX1 WDR1 VIM B4GALT1 PTRF PTTG1IP KCND2 IFI35 TGFBI TGFBI RPL37A PIGT TPTE FNDC3B KRT8P12 PAAF1 TMEM214 DNM3 CXCL1 ACTA2 STK17A TOM1 HRH1 DPF1 HERPUD1 MTHFD2L ANXA2 THAP10 LPP BASP1 DPF1 PYGL RAP1GAP ALDH3B1 SMAD1 DUSP26 ANXA2 SLC43A3 C10orf137 SATB1 FCGBP DES CD55 SLC30A9 TAGLN C11orf2 CSNK1D PGGT1B LRRC47 AKIRIN2 EML1 REXO2 MMP8 COG2 TAGLN GNS WDR1 CR1 WDR47 MINA AIM1 NFYB PTRF ZNF821 NEURL ERLIN2 TSKS OSMR RNF220 SC5DL KCNJ3 TNFAIP6 C11orf24 APLP2 LYN CYTIP BHLHE40 RAB7L1 PTRF SHC1 LRP10 DTX3 RUFY1 FNDC3B LYN NFE2L1 ZNF248 UGCG GLT25D1 HRH1 RERGL TRAM2 ENSG00000230551 HMOX1 LTBP3 SLC35F2 LRP10 LIN7B

56 A2M ELL2 FKBP1B LGALS1 FNDC3B ARMCX5 LPP IL8 PROS1 PYGL GLRX KLF6 KLHDC3 ZNF248 TMEM8A PTX3 ACTA2 HNRNPAB FABP6 MMP12 IGF2R CD151 HRH1 ZFP36L2 SLC43A3 RAB20 SERPINE1 C21orf62 GPR45 TMBIM6 FCGBP LGALS1 ENSG00000234745 POSTN LPP CDH9 FAM171A1 PYGL NRP1 CSRNP3 ZFP36 TNFRSF1A TUBG2 PTX3 C1R CTSB CEP68 FILIP1L TM9SF1 FCGBP COPB2 ADAM9 CTSB ANXA3 PLCD1 IFI30 NDST4 LDOC1 ADPGK TGFB2 TRIP6 CSNK1D CHI3L1 FEM1C MYH10 PALM2‐AKAP2 AEBP1 ASB8 CTSA VAMP1 PTP4A2 SERINC3 GNS SLC39A8 MYOF SENP5 KLHL23 CDH18 WDR47 GNS LASS2 MAPK8IP2 PRF1 AJAP1 SEMA4A SLC16A3 NKRF SQRDL PDK3 IGFBP5 ENDOD1 ZNF287 LRRFIP1 HDAC2 SQRDL STAT3 RUNDC3A CHI3L2 DDX25 REEP1 IFT27 RCAN1 CABYR MARCKSL1 FAM120A LRRC20 LRRC49 MYT1L GAD2 TNFAIP2 HDAC9 TRIM23 ACCN2 CTNNA1 WIF1 CASP4 NFKB1 OSMR NUAK2 CREB3L2 OSBPL1A C1orf113 PKMYT1 STMN4 EHD2 MCL1 EHD2 NCAN SERPINA1 EXT2 BCL2A1 ARL4C LIMS1 BHLHE40 PRPSAP2 RAPGEF4 ICAM1 RUNDC3B LRRC8B SHC1 PIN1

57 EFEMP2 LIMS1 KIAA1107 CLCF1 TIPARP RANBP17 GLT25D1 SIL1 TAF11 H2AFY RAPGEF4 ZNF280D RNF8 BATF YKT6 PJA1 NPAS2 CD81 PLSCR1 NRXN1 PLEKHB2 CA3 HK3 NAGLU VCL FAM182B MAPKAPK2 NAB1 SH3BGRL3 ENSG00000231925 RAB21 FCRL2 IFI16 LTBP3 RUNX1 PLXND1 QTRTD1 TGOLN2 FAM46A ITGA3 MMP19 PHC2 ATP2C2 BACE2 IQGAP1 SLC25A44 C17orf91 CALD1 ANXA1 CEP97 RNF208 FAM98A PCK2 MAN1C1 PROS1 RAB27A CD99 MRC2 ANXA1 STEAP3 PALLD ASCL1 SERPINH1 GSTA4 GTPBP2 C10orf88 DAP CXCL3 ACP2 TAGLN2 GSTA4 RPL31 C9orf91 HMGCS1 TOMM20 ANXA5 ACSL6 MAPKAP1 SDCBP MUC1 USP33 ZFP36L2 TMEM109 CYR61 SERPINE1 HEXB SYNPO PLXNB2 SERPINE1 ATP5L TMBIM6 GNA15 RNF11 MXRA8 DLGAP1 ABCC3 FAM188B DEAF1 PDZRN4 KIAA0513 TMBIM1 STX4 ATP5C1 COX11 NEDD9 TNFRSF1A MXRA8 UBB KIF21B C1orf38 ENSG00000205073 C1R VDR VEGFA GALC PLIN2 NUCB1 COPB2 NRP1 MYH9 SRPX2 TGM2 CA12 DNAJB1 FLRT1 FOSL2 ENSG00000090857 TNFRSF1A ATPIF1 IDUA RRAS PKM2 LRP2BP PTCH1 CACYBP TNFAIP3 ATP5A1 TIPRL CHI3L1 PARVB TPP1

58 ATP1B1 C1R GRN BOLA1 SRPX2 MVP NECAP1 DYRK3 MSN TGFB1I1 CXCL2 CPD RGS7 TNFAIP3 STAB1 CCDC109B CHI3L1 RHOT1 GBP2 RRAS2 ENSG00000163430 SEMA6B SWAP70 DYNC1LI1 TMED9 PIK3R5 C3 DENND1B DSE CDR1 MYOF CCDC109B C1S S100A11 GBP2 CHSY1 CDH18 PIK3C2B ADM ENSG00000204681 CTSA HLA‐C LMNA PLK3 NRP2 NKRF IL10RA SKP1 TNFRSF12A MYOF ST3GAL6 ATP2B2 ACTG2 ACTN1 NFE2L2 ERBB4 LAMC1 NNMT S100A11 ENSG00000156976 RCAN1 MT1G IRAK1 PLP2 PI3 RAB26 PARG SERPINB1 P4HB IRF1 PLA2G2A RNASEH2B UPP1 LASS2 VDAC3 KCTD12 KAT2B GPC4 RPS27L LMNA FLNA ITGB8 RNASE4 C12orf24 CTNNA1 P4HA2 ABCA1 RBM47 CXCL6 CFLAR FAS SLIT1 ASB13 NRXN2 GLUL ARL3 SFRP4 LRRFIP1 NDUFS1 SCAMP5 S100B C10orf10 SRPK1 DDX25 HSPA5 TERF2 CITED2 SPHAR SPATS2 ATP2B2 LAMB1 SLC8A2 SEC24D HSPH1 CCL2 KHNYN POLB SEPHS2 NNMT THTPA ENOX1 PLP2 FBLN5 PTPRE APPBP2 ANGPT2 ARSJ GDAP2 NMT2 PLAUR SLPI ENSG00000111684 IDI1 IRF1 FBXO9 THRA MYO1C PPP3CB TKTL1 UPP1 BTG1

59 RALGPS1 PIP4K2B PDIA5 IPO4 TGFB1 UBE2H DMXL2 MT4 TNC CHRDL1 BCAN DPY19L1 ZMYND11 RBM47 IL6ST DPYD NFKB1 MAGEH1 KIAA1107 TSPO COL6A1 EFEMP1 MCL1 PLTP FGF9 VPS13A ENSG00000217930 CIT TERF2 GUSB SH3GLB1 C1orf61 EMP3 TRIP10 CCL2 FLII CD44 SLC1A4 RIPK1 WNT7B RGS2 COL4A1 ZNF280D PLAUR ENSG00000196459 C10orf18 PTGS2 TMEM43 JUN RALGPS1 LGALS3BP BZRAP1 RNASE2 PLAU SMPDL3A KIAA1797 S100A9 PRDM10 MLXIP NPY5R PRDM16 NAGLU F13A1 DLG3 DPYD FZD7 EFEMP1 ENSA RANBP17 PITPNM1 CD44 NMI TLR2 ENSG00000133606 PLAU KIAA1033 IRF2 CXXC4 SOD3 BCL3 SPSB1 GAP43 CST7 FAM129A IFITM2 KCNMA1 MYL9 DOPEY2 ENSG00000231925 NAMPT FCER1G NAP1L3 IFI16 NUDT11 DDR2 FAM46A PRDM1 PLIN3 CXXC4 IQGAP1 BCL3 CALD1 MMP1 CUEDC2 FAM129A ASRGL1 MCTP2 MAN1C1 NFKBIA PMP22 ABAT

60 OMG CCR1 CD99 NAMPT STEAP3 FEZ1 TIMP1 LY96 FLNC NUDT11 C11orf67 ITPKC C21orf7 LEPREL1 C10orf88 CDKN1A PTPN4 TNFSF13 COL4A3BP PLIN3 MAP2K3 ANXA4 PCSK5 C1orf183 TOMM20 CTCF FRS3 IL6R SPATS2L SNRPN MCF2L2 IQGAP1 MAP2K6 ASRGL1 RAB33A CLEC7A PEPD RAC2 LOXL1 SHB PLEKHA4 AHCYL2 LGALS3 PMP22 SYNPO STEAP3 SERPINA3 TIMP1 CDK5R1 RELB RNFT2 FRS3 SLITRK5 THBS1 AHNAK ZMYM6 ABCC3 USP33 EMP1 TREM1 ENSG00000060138 CDC14A NAV3 PRCP RNF187 POLR3B PAN2 LGALS3 PHYHIP SYNPO GFOD2 CCT6B TDRKH CDK5R1 ID3 RNFT2 GDF9 SOAT1 DIRAS3 ABCC3 C9orf125 ENSG00000060138 SERPING1 MR1 SUCLG2 SLC39A14 PAK7 GFOD2 CEBPB KLF11 BCL7A PIM1 NRCAM TDO2

61 IGFBP7 MAFB NEDD9 TCF12 NKX2‐1 PRKACB DYNC1I1 SERPING1 RBM9 BCL7A R3HDM1 CEBPB RIBC2 MAP2 PYCR1 KLF4 CAND1 ENSG00000150687 PPP3R1 LAMP2 PPP1R7 R3HDM1 GNG12 IBSP SLC25A22 UAP1 LIF LIF TEAD3 CCL20 GPC1 MYH9 FOSL2 SBNO2 FAAH CA12 S100A10 FOSL2 ATPIF1 S100A10 CD63 RCN3 YAP1 IL6 LTF IL15RA RAB3A LTF B4GALT5 FOSL1 RIC3 DKK3 SLC6A12 PKM2 CACYBP TRADD LZTS1 COL1A1 COQ2 VPS45 INO80B CXCR4 SEC61A2 OLIG2 PPFIA2 TPP1 RPS6KA5 RET ATP1A3 SLC2A3 GPR22 ATMIN PPP2R5D C1orf21 MSRB2 NDRG1 TMEM35 IGFBP4 CLASP2 PAFAH1B3 AR MVP TMED10 TIMP2 SRPK3 TMEM35 MSN RHOH UPF2 ZBED5 SH3BP2 TES RTF1 ESRRG

62 TPM4 FPR1 FAR2 MSN HAGH PSAT1 KCNA3 SCRT1 EHD4 NSMAF RHOT1 TPM4 ENSG00000163430 POLD4 ACSS3 CUL3 MYL12A SRPR CHN1 ADAM12 DYNC1LI1 TRIM38 C3 SLC22A4 C1S DUSP3 PLCH2 FSD1 CHSY1 C1S CHST2 NOL4 CEBPG CAMSAP1L1 CSTF2T SLC16A10 AACS MEF2D PDPN TCIRG1 SPARC PTPRK RYR1 PDPN SCN10A SLC22A18 NECAP2 NRP2 ARHGEF11 ENSG00000204642 LIMA1 BLVRB GNAO1 FCGR2B CSTA CSTA FUT9 CXCL5 PLCL2 STAT5A ACTN1 IL1R1 ENSG00000156976 HOXB6 S100A6 EHBP1L1 ACTR1A CD14 TEAD1 SIGLEC7 RAB26 RHBDF2 KIAA0427 RAB26 PHLPP2 WAS DUSP6 COL1A2 DLG4 COPZ2 GPC4 CPA4 TMEM22 EDNRB FLNA ABCA1 KIAA1045 ZNF217 FAM76A SOD2 C12orf24 KCNE4 ABCA1 WWTR1

63 ZNF217 PODXL2 WWTR1 DGAT1 ASB13 TSPAN31 IDS ENSG00000204516 CFI ENSG00000015479 ENSG00000213719 KIAA0247 ARL3 CFI IL13RA1 ENSG00000213719 PPP1R12B CTSL1 CBARA1 TACC2 WLS GCLM ANKRD26 C10orf10 CD163 IL13RA1 MAPK10 DCC ZFP36L1 C9orf167 HSPH1 MYC PLAT HSPA5 FJX1 TRIB1 EIF4ENIF1 SDCCAG8 ENSG00000166503 IL4R FBLN5 TSPAN4 ITGA5 CD163 CHRNA9 DDIT4 MTMR15 ZFP36L1 CAPG GALNT2 OXCT1 ITGA5 ENSG00000111684 LAPTM5 CBLN1 C6orf208 PAK3 SIGLEC9 ARL5A MT2A PPP3CB FDFT1 UGP2 ENSG00000204592 ITGA7 MPPED2 CLIC4 GLIPR1 PHGDH HP PRKCB ARPC1B TRIM32 GRSF1 ARHGEF9 ENSG00000137331 CAPN2 DUSP1 TNC CP SDC4 KYNU NMD3 FAH C8orf4 NOD2 ZYX CLEC2B CUL2 SLC11A1 AMPH JUNB JPH3 G0S2

64 PAM CBR4 COL6A1 VWA5A PHACTR1 TIMM22 RAP2B COL6A2 DRAM1 DRAM1 INA CH25H MBNL2 SCHIP1 SLC2A10 DDAH1 TRIM37 CDCP1 PLTP TRIM37 FAM163A PLTP FIG4 ELF4 HS2ST1 SCAI CNIH3 MAP6D1 CNN1 TCF15 EMP3 EMP3 C13orf18 F7 C1RL WIPI1 PIK3R2 NPC2 MTDH C1RL CLEC5A ENSG00000235280 SH3GL3 SLC39A1 RIPK1 CLEC5A IL1RAP BIRC3 TTC13 TNFRSF1B ENSG00000196459 COL6A3 ZNF238 SAT1 THBD PNMAL1 GFPT2 HLX LAIR1 MGAT1 SRGAP3 LGALS3BP

65 Supp. Table S2: TAZ expression (Affymetrix) in TCGA and tumor survival prediction stratified by subtype

Verhaak Class (Called) Sample number p value (Cox proportional hazard model)

PN 54 0.0011 MES 53 0.57 Neural 25 0.64 Classical 50 0.98 Total 182 0.00053

Verhaak Class (Calculated) Sample number p value (Cox proportional hazard model)

PN 80 6.90E‐05 MES 126 0.015 Neural 67 0.5 Classical 116 0.75 Total 389 4.90E‐05

66 Supp Table S3A: Genes upregulated by 4SA by 1.5 fold or greater

Gene symbol 4SAminV Ensembl ID Description Column1 Column2 Column3 Column4 Column5 Column6 CTGF 8.628846629 ENSG00000118523 connective tissue growth factor [Source:HGNC Symbol;Acc:2500] FLG 7.726953298 ENSG00000143631 filaggrin [Source:HGNC Symbol;Acc:3748] MFAP5 6.498700493 ENSG00000197614 microfibrillar associated protein 5 [Source:HGNC Symbol;Acc:29673] KRT5 6.070990129 ENSG00000186081 keratin 5 [Source:HGNC Symbol;Acc:6442] ADAMTS1 5.988296915 ENSG00000154734 ADAM metallopeptidase with thrombospondin type 1 motif, 1 [Source:HGNC Symbol;Acc:217] MET 5.791805246 ENSG00000105976 met proto‐oncogene (hepatocyte growth factor receptor) [Source:HGNC Symbol;Acc:7029] AOX1 5.321222757 ENSG00000138356 aldehyde oxidase 1 [Source:HGNC Symbol;Acc:553] PCLO 5.131317793 ENSG00000186472 piccolo (presynaptic cytomatrix protein) [Source:HGNC Symbol;Acc:13406] ADAMTS5 5.096595415 ENSG00000154736 ADAM metallopeptidase with thrombospondin type 1 motif, 5 [Source:HGNC Symbol;Acc:221] ADRB2 5.076314529 ENSG00000169252 adrenergic, beta‐2‐, receptor, surface [Source:HGNC Symbol;Acc:286] SERPINB7 4.935536023 ENSG00000166396 serpin peptidase inhibitor, clade B (ovalbumin), member 7 [Source:HGNC Symbol;Acc:13902] SEMA3C 4.764860544 ENSG00000075223 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C PMAIP1 4.666707618 ENSG00000141682 phorbol‐12‐myristate‐13‐acetate‐induced protein 1 [Source:HGNC Symbol;Acc:9108] LUM 4.59876721 ENSG00000139329 lumican [Source:HGNC Symbol;Acc:6724] LCP1 4.59403671 ENSG00000136167 lymphocyte cytosolic protein 1 (L‐plastin) [Source:HGNC Symbol;Acc:6528] NAV3 4.482289343 ENSG00000067798 neuron navigator 3 [Source:HGNC Symbol;Acc:15998] SCG5 4.453066048 ENSG00000166922 secretogranin V (7B2 protein) [Source:HGNC Symbol;Acc:10816] TGFBI 4.36309314 ENSG00000120708 transforming growth factor, beta‐induced, 68kDa [Source:HGNC Symbol;Acc:11771] CYP1B1 4.332478958 ENSG00000138061 cytochrome P450, family 1, subfamily B, polypeptide 1 [Source:HGNC Symbol;Acc:2597] KRT34 4.214110469 ENSG00000131737 keratin 34 [Source:HGNC Symbol;Acc:6452] SNAPC1 4.206985296 ENSG00000023608 small nuclear RNA activating complex, polypeptide 1, 43kDa [Source:HGNC Symbol;Acc:11134] F2RL1 4.085288805 ENSG00000164251 coagulation factor II (thrombin) receptor‐like 1 [Source:HGNC Symbol;Acc:3538] S1PR1 4.057415023 ENSG00000170989 sphingosine‐1‐phosphate receptor 1 [Source:HGNC Symbol;Acc:3165] KIT 4.035506367 ENSG00000157404 v‐kit Hardy‐Zuckerman 4 feline sarcoma viral oncogene homolog [Source:HGNC Symbol;Acc:6342] LOX 3.993249479 ENSG00000113083 lysyl oxidase [Source:HGNC Symbol;Acc:6664] ENPP2 3.949094802 ENSG00000136960 ectonucleotide pyrophosphatase/phosphodiesterase 2 [Source:HGNC Symbol;Acc:3357] ESM1 3.91562721 ENSG00000164283 endothelial cell‐specific molecule 1 [Source:HGNC Symbol;Acc:3466] ST6GALNAC5 3.883072208 ENSG00000117069 ST6 (alpha‐N‐acetyl‐neuraminyl‐2,3‐beta‐galactosyl‐1,3)‐N‐acetylgalactosaminide alpha‐2,6‐sialyltransferase 5 C7 3.846260514 ENSG00000112936 complement component 7 [Source:HGNC Symbol;Acc:1346] HAPLN1 3.793449084 ENSG00000145681 hyaluronan and proteoglycan link protein 1 [Source:HGNC Symbol;Acc:2380] PTGER4 3.719236999 ENSG00000171522 prostaglandin E receptor 4 (subtype EP4) [Source:HGNC Symbol;Acc:9596]

67 PTHLH 3.715653776 ENSG00000087494 parathyroid hormone‐like hormone [Source:HGNC Symbol;Acc:9607] PTPRR 3.688865348 ENSG00000153233 protein tyrosine phosphatase, receptor type, R [Source:HGNC Symbol;Acc:9680] OLFML3 3.612651135 ENSG00000116774 olfactomedin‐like 3 [Source:HGNC Symbol;Acc:24956] HS3ST2 3.574432104 ENSG00000122254 heparan sulfate (glucosamine) 3‐O‐sulfotransferase 2 [Source:HGNC Symbol;Acc:5195] ZNF185 3.556887465 ENSG00000147394 zinc finger protein 185 (LIM domain) [Source:HGNC Symbol;Acc:12976] CD55 3.551598049 ENSG00000196352 CD55 molecule, decay accelerating factor for complement (Cromer blood group) [Source:HGNC Symbol;Acc:2665] NOX4 3.538477142 ENSG00000086991 NADPH oxidase 4 [Source:HGNC Symbol;Acc:7891] IL13RA2 3.504930089 ENSG00000123496 interleukin 13 receptor, alpha 2 [Source:HGNC Symbol;Acc:5975] TMEM90B 3.502558873 ENSG00000101463 transmembrane protein 90B [Source:HGNC Symbol;Acc:15885] HOXB6 3.412277849 ENSG00000108511 homeobox B6 [Source:HGNC Symbol;Acc:5117] DSC1 3.397924529 ENSG00000134765 desmocollin 1 [Source:HGNC Symbol;Acc:3035] FGF13 3.373828072 ENSG00000129682 fibroblast growth factor 13 [Source:HGNC Symbol;Acc:3670] PLAUR 3.355803598 ENSG00000011422 plasminogen activator, urokinase receptor [Source:HGNC Symbol;Acc:9053] KRT33B 3.317208178 ENSG00000131738 keratin 33B [Source:HGNC Symbol;Acc:6451] TUFT1 3.219899854 ENSG00000143367 tuftelin 1 [Source:HGNC Symbol;Acc:12422] CPA4 3.199085071 ENSG00000128510 carboxypeptidase A4 [Source:HGNC Symbol;Acc:15740] PALMD 3.126896571 ENSG00000099260 palmdelphin [Source:HGNC Symbol;Acc:15846] BCAR3 3.098567898 ENSG00000137936 breast cancer anti‐estrogen resistance 3 [Source:HGNC Symbol;Acc:973] IL1B 3.083991296 ENSG00000125538 interleukin 1, beta [Source:HGNC Symbol;Acc:5992] MAN1A1 3.071521389 ENSG00000111885 mannosidase, alpha, class 1A, member 1 [Source:HGNC Symbol;Acc:6821] PSTPIP2 3.036399823 ENSG00000152229 proline‐serine‐threonine phosphatase interacting protein 2 [Source:HGNC Symbol;Acc:9581] MYL1 3.031148908 ENSG00000168530 myosin, light chain 1, alkali; skeletal, fast [Source:HGNC Symbol;Acc:7582] PROCR 3.028573364 ENSG00000101000 protein C receptor, endothelial [Source:HGNC Symbol;Acc:9452] COL11A1 3.014201497 ENSG00000060718 collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186] STEAP1 2.969702523 ENSG00000164647 six transmembrane epithelial antigen of the prostate 1 [Source:HGNC Symbol;Acc:11378] EXPH5 2.96477722 ENSG00000110723 exophilin 5 [Source:HGNC Symbol;Acc:30578] CH25H 2.862008059 ENSG00000138135 cholesterol 25‐hydroxylase [Source:HGNC Symbol;Acc:1907] LEPREL1 2.86199766 ENSG00000090530 leprecan‐like 1 [Source:HGNC Symbol;Acc:19317] RGS7 2.85523525 ENSG00000182901 regulator of G‐protein signaling 7 [Source:HGNC Symbol;Acc:10003] EDN1 2.849418893 ENSG00000078401 endothelin 1 [Source:HGNC Symbol;Acc:3176] RYR2 2.840398456 ENSG00000198626 ryanodine receptor 2 (cardiac) [Source:HGNC Symbol;Acc:10484] STXBP6 2.806254424 ENSG00000168952 syntaxin binding protein 6 (amisyn) [Source:HGNC Symbol;Acc:19666] CFI 2.772647488 ENSG00000205403 complement factor I [Source:HGNC Symbol;Acc:5394] COL6A3 2.753600711 ENSG00000163359 collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]

68 TPM1 2.732755129 ENSG00000140416 tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010] MATN3 2.690707835 ENSG00000132031 matrilin 3 [Source:HGNC Symbol;Acc:6909] VIPR1 2.650270672 ENSG00000114812 vasoactive intestinal peptide receptor 1 [Source:HGNC Symbol;Acc:12694] C6orf15 2.633647196 ENSG00000204542 chromosome 6 open reading frame 15 [Source:HGNC Symbol;Acc:13927] ALCAM 2.568146557 ENSG00000170017 activated leukocyte cell adhesion molecule [Source:HGNC Symbol;Acc:400] AMIGO2 2.555956738 ENSG00000139211 adhesion molecule with Ig‐like domain 2 [Source:HGNC Symbol;Acc:24073] PLK2 2.538925818 ENSG00000145632 polo‐like kinase 2 [Source:HGNC Symbol;Acc:19699] LRRC2 2.526408329 ENSG00000163827 leucine rich repeat containing 2 [Source:HGNC Symbol;Acc:14676] ADORA2B 2.514845031 ENSG00000170425 adenosine A2b receptor [Source:HGNC Symbol;Acc:264] AIM1 2.505416309 ENSG00000112297 absent in melanoma 1 [Source:HGNC Symbol;Acc:356] KCNN4 2.484985904 ENSG00000104783 potassium intermediate/small conductance calcium‐activated channel, subfamily N, member 4 FAM129A 2.481795422 ENSG00000135842 family with sequence similarity 129, member A [Source:HGNC Symbol;Acc:16784] GPRC5A 2.407533035 ENSG00000013588 G protein‐coupled receptor, family C, group 5, member A [Source:HGNC Symbol;Acc:9836] MBNL2 2.337533642 ENSG00000139793 muscleblind‐like 2 (Drosophila) [Source:HGNC Symbol;Acc:16746] MYH9 2.320226507 ENSG00000100345 myosin, heavy chain 9, non‐muscle [Source:HGNC Symbol;Acc:7579] CD44 2.31069685 ENSG00000026508 CD44 molecule (Indian blood group) [Source:HGNC Symbol;Acc:1681] RAB3B 2.293771755 ENSG00000169213 RAB3B, member RAS oncogene family [Source:HGNC Symbol;Acc:9778] PORCN 2.271270038 ENSG00000102312 porcupine homolog (Drosophila) [Source:HGNC Symbol;Acc:17652] DEPDC6 2.268192338 ENSG00000155792 DEP domain containing 6 [Source:HGNC Symbol;Acc:22953] VEGFC 2.266713293 ENSG00000150630 vascular endothelial growth factor C [Source:HGNC Symbol;Acc:12682] PKP2 2.24722349 ENSG00000057294 plakophilin 2 [Source:HGNC Symbol;Acc:9024] STX3 2.219609637 ENSG00000166900 syntaxin 3 [Source:HGNC Symbol;Acc:11438] LY96 2.21422835 ENSG00000154589 lymphocyte antigen 96 [Source:HGNC Symbol;Acc:17156] KLF5 2.208028118 ENSG00000102554 Kruppel‐like factor 5 (intestinal) [Source:HGNC Symbol;Acc:6349] CAV2 2.200578003 ENSG00000105971 caveolin 2 [Source:HGNC Symbol;Acc:1528] IL11 2.165967487 ENSG00000095752 interleukin 11 [Source:HGNC Symbol;Acc:5966] NT5E 2.157479577 ENSG00000135318 5'‐nucleotidase, ecto (CD73) [Source:HGNC Symbol;Acc:8021] SP140L 2.157119947 ENSG00000185404 SP140 nuclear body protein‐like [Source:HGNC Symbol;Acc:25105] ABL2 2.137723618 ENSG00000143322 v‐abl Abelson murine leukemia viral oncogene homolog 2 [Source:HGNC Symbol;Acc:77] BST1 2.129156539 ENSG00000109743 bone marrow stromal cell antigen 1 [Source:HGNC Symbol;Acc:1118] GAS6 2.117679276 ENSG00000183087 growth arrest‐specific 6 [Source:HGNC Symbol;Acc:4168] PDE1C 2.089378888 ENSG00000154678 phosphodiesterase 1C, calmodulin‐dependent 70kDa [Source:HGNC Symbol;Acc:8776] CD34 2.083576955 ENSG00000174059 CD34 molecule [Source:HGNC Symbol;Acc:1662] TBC1D9 2.072743846 ENSG00000109436 TBC1 domain family, member 9 (with GRAM domain) [Source:HGNC Symbol;Acc:21710]

69 ACTG2 2.032821246 ENSG00000163017 actin, gamma 2, smooth muscle, enteric [Source:HGNC Symbol;Acc:145] SLC3A2 2.029995526 ENSG00000168003 solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 NUAK2 2.02489907 ENSG00000163545 NUAK family, SNF1‐like kinase, 2 [Source:HGNC Symbol;Acc:29558] DRAM1 2.02350602 ENSG00000136048 DNA‐damage regulated autophagy modulator 1 [Source:HGNC Symbol;Acc:25645] PTPN14 1.994273777 ENSG00000152104 protein tyrosine phosphatase, non‐receptor type 14 [Source:HGNC Symbol;Acc:9647] HHAT 1.980800477 ENSG00000054392 hedgehog acyltransferase [Source:HGNC Symbol;Acc:18270] BMP4 1.934043317 ENSG00000125378 bone morphogenetic protein 4 [Source:HGNC Symbol;Acc:1071] DGKA 1.906340161 ENSG00000065357 diacylglycerol kinase, alpha 80kDa [Source:HGNC Symbol;Acc:2849] SGCG 1.896458121 ENSG00000102683 sarcoglycan, gamma (35kDa dystrophin‐associated glycoprotein) [Source:HGNC Symbol;Acc:10809] PAM 1.893260524 ENSG00000145730 peptidylglycine alpha‐amidating monooxygenase [Source:HGNC Symbol;Acc:8596] GNG11 1.893233494 ENSG00000127920 guanine nucleotide binding protein (G protein), gamma 11 [Source:HGNC Symbol;Acc:4403] PCP4 1.88410012 ENSG00000183036 Purkinje cell protein 4 [Source:HGNC Symbol;Acc:8742] BNC2 1.869213371 ENSG00000173068 basonuclin 2 [Source:HGNC Symbol;Acc:30988] MAL 1.85701867 ENSG00000172005 mal, T‐cell differentiation protein [Source:HGNC Symbol;Acc:6817] PRKAG2 1.830936283 ENSG00000106617 protein kinase, AMP‐activated, gamma 2 non‐catalytic subunit [Source:HGNC Symbol;Acc:9386] IL4R 1.827893511 ENSG00000077238 interleukin 4 receptor [Source:HGNC Symbol;Acc:6015] NMNAT2 1.816179787 ENSG00000157064 nicotinamide nucleotide adenylyltransferase 2 [Source:HGNC Symbol;Acc:16789] COL10A1 1.81532772 ENSG00000123500 collagen, type X, alpha 1 [Source:HGNC Symbol;Acc:2185] RNF128 1.794012803 ENSG00000133135 ring finger protein 128 [Source:HGNC Symbol;Acc:21153] LIPG 1.774191492 ENSG00000101670 lipase, endothelial [Source:HGNC Symbol;Acc:6623] HSPB8 1.767346263 ENSG00000152137 heat shock 22kDa protein 8 [Source:HGNC Symbol;Acc:30171] MAP3K14 1.757288463 ENSG00000006062 mitogen‐activated protein kinase kinase kinase 14 [Source:HGNC Symbol;Acc:6853] COL1A2 1.749698803 ENSG00000164692 collagen, type I, alpha 2 [Source:HGNC Symbol;Acc:2198] CITED2 1.738288027 ENSG00000164442 Cbp/p300‐interacting transactivator, with Glu/Asp‐rich carboxy‐terminal domain, 2 [Source:HGNC Symbol;Acc:1987] PLAGL1 1.731897741 ENSG00000118495 pleiomorphic adenoma gene‐like 1 [Source:HGNC Symbol;Acc:9046] SDPR 1.726554679 ENSG00000168497 serum deprivation response [Source:HGNC Symbol;Acc:10690] PERP 1.714143994 ENSG00000112378 PERP, TP53 apoptosis effector [Source:HGNC Symbol;Acc:17637] GBP1 1.702848709 ENSG00000117228 guanylate binding protein 1, interferon‐inducible, 67kDa [Source:HGNC Symbol;Acc:4182] ABCA1 1.686125152 ENSG00000165029 ATP‐binding cassette, sub‐family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29] KCNJ8 1.670698362 ENSG00000121361 potassium inwardly‐rectifying channel, subfamily J, member 8 [Source:HGNC Symbol;Acc:6269] GTF2F2 1.659620864 ENSG00000188342 general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653] ACTN1 1.642667183 ENSG00000072110 actinin, alpha 1 [Source:HGNC Symbol;Acc:163] AK5 1.620205699 ENSG00000154027 adenylate kinase 5 [Source:HGNC Symbol;Acc:365] WWC2 1.607905353 ENSG00000151718 WW and C2 domain containing 2 [Source:HGNC Symbol;Acc:24148]

70 GCNT1 1.593751494 ENSG00000187210 glucosaminyl (N‐acetyl) transferase 1, core 2 [Source:HGNC Symbol;Acc:4203] NEK7 1.591590555 ENSG00000151414 NIMA (never in mitosis gene a)‐related kinase 7 [Source:HGNC Symbol;Acc:13386] IGF1 1.57547068 ENSG00000017427 insulin‐like growth factor 1 (somatomedin C) [Source:HGNC Symbol;Acc:5464] PHACTR2 1.569614448 ENSG00000112419 phosphatase and actin regulator 2 [Source:HGNC Symbol;Acc:20956] ACOT9 1.518181977 ENSG00000123130 acyl‐CoA thioesterase 9 [Source:HGNC Symbol;Acc:17152] NAMPT 1.512328728 ENSG00000105835 nicotinamide phosphoribosyltransferase [Source:HGNC Symbol;Acc:30092] UAP1 1.51072148 ENSG00000117143 UDP‐N‐acteylglucosamine pyrophosphorylase 1 [Source:HGNC Symbol;Acc:12457] IL7R 1.504271721 ENSG00000168685 interleukin 7 receptor [Source:HGNC Symbol;Acc:6024] EREG 1.490897183 ENSG00000124882 epiregulin [Source:HGNC Symbol;Acc:3443] SERPINB8 1.47960065 ENSG00000166401 serpin peptidase inhibitor, clade B (ovalbumin), member 8 [Source:HGNC Symbol;Acc:8952] STAC 1.479340418 ENSG00000144681 SH3 and cysteine rich domain [Source:HGNC Symbol;Acc:11353] ABLIM3 1.464883205 ENSG00000173210 actin binding LIM protein family, member 3 [Source:HGNC Symbol;Acc:29132] SKAP1 1.46170796 ENSG00000141293 src kinase associated phosphoprotein 1 [Source:HGNC Symbol;Acc:15605] C9orf3 1.45518789 ENSG00000148120 chromosome 9 open reading frame 3 [Source:HGNC Symbol;Acc:1361] PAWR 1.449764164 ENSG00000177425 PRKC, apoptosis, WT1, regulator [Source:HGNC Symbol;Acc:8614] TPMT 1.448024992 ENSG00000137364 thiopurine S‐methyltransferase [Source:HGNC Symbol;Acc:12014] AQP1 1.440291151 ENSG00000240583 aquaporin 1 (Colton blood group) [Source:HGNC Symbol;Acc:633] SLC10A3 1.418157823 ENSG00000126903 solute carrier family 10 (sodium/bile acid cotransporter family), member 3 [Source:HGNC Symbol;Acc:22979] ANKRD1 1.414930636 ENSG00000148677 ankyrin repeat domain 1 (cardiac muscle) [Source:HGNC Symbol;Acc:15819] ANGPT1 1.408223801 ENSG00000154188 angiopoietin 1 [Source:HGNC Symbol;Acc:484] GPC4 1.40247277 ENSG00000076716 glypican 4 [Source:HGNC Symbol;Acc:4452] VDR 1.402061204 ENSG00000111424 vitamin D (1,25‐ dihydroxyvitamin D3) receptor [Source:HGNC Symbol;Acc:12679] HPS5 1.399805901 ENSG00000110756 Hermansky‐Pudlak syndrome 5 [Source:HGNC Symbol;Acc:17022] TES 1.397551256 ENSG00000135269 testis derived transcript (3 LIM domains) [Source:HGNC Symbol;Acc:14620] CXCL2 1.387198424 ENSG00000081041 chemokine (C‐X‐C motif) ligand 2 [Source:HGNC Symbol;Acc:4603] SMAD7 1.382388492 ENSG00000101665 SMAD family member 7 [Source:HGNC Symbol;Acc:6773] GRIA1 1.377061503 ENSG00000155511 glutamate receptor, ionotropic, AMPA 1 [Source:HGNC Symbol;Acc:4571] SLC25A24 1.363357007 ENSG00000085491 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24 [Source:HGNC Symbol;Acc:20662] TGFBR2 1.36045341 ENSG00000163513 transforming growth factor, beta receptor II (70/80kDa) [Source:HGNC Symbol;Acc:11773] MAP1LC3B 1.3522753 ENSG00000140941 microtubule‐associated protein 1 light chain 3 beta [Source:HGNC Symbol;Acc:13352] SLC1A5 1.350951003 ENSG00000105281 solute carrier family 1 (neutral amino acid transporter), member 5 [Source:HGNC Symbol;Acc:10943] RAB11FIP5 1.35056155 ENSG00000135631 RAB11 family interacting protein 5 (class I) [Source:HGNC Symbol;Acc:24845] TNNT1 1.341150285 ENSG00000105048 troponin T type 1 (skeletal, slow) [Source:HGNC Symbol;Acc:11948] ETS1 1.335921748 ENSG00000134954 v‐ets erythroblastosis virus E26 oncogene homolog 1 (avian) [Source:HGNC Symbol;Acc:3488]

71 KIF17 1.333431607 ENSG00000117245 kinesin family member 17 [Source:HGNC Symbol;Acc:19167] ELL2 1.333120348 ENSG00000118985 elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064] BLVRB 1.325595266 ENSG00000090013 biliverdin reductase B (flavin reductase (NADPH)) [Source:HGNC Symbol;Acc:1063] MOXD1 1.31298716 ENSG00000079931 monooxygenase, DBH‐like 1 [Source:HGNC Symbol;Acc:21063] DUSP3 1.312735704 ENSG00000108861 dual specificity phosphatase 3 [Source:HGNC Symbol;Acc:3069] CREB3L1 1.311927403 ENSG00000157613 cAMP responsive element binding protein 3‐like 1 [Source:HGNC Symbol;Acc:18856] MYO1C 1.305485115 ENSG00000197879 myosin IC [Source:HGNC Symbol;Acc:7597] FSTL1 1.303011006 ENSG00000163430 follistatin‐like 1 [Source:HGNC Symbol;Acc:3972] FGF5 1.302911006 ENSG00000138675 fibroblast growth factor 5 [Source:HGNC Symbol;Acc:3683] SEMA3A 1.287389233 ENSG00000075213 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A RPS6KA4 1.281847937 ENSG00000162302 ribosomal protein S6 kinase, 90kDa, polypeptide 4 [Source:HGNC Symbol;Acc:10433] LONRF3 1.278375064 ENSG00000175556 LON peptidase N‐terminal domain and ring finger 3 [Source:HGNC Symbol;Acc:21152] FZD2 1.278202787 ENSG00000180340 frizzled homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:4040] NEU1 1.277309624 ENSG00000204386 sialidase 1 (lysosomal sialidase) [Source:HGNC Symbol;Acc:7758] HSD17B2 1.273225835 ENSG00000086696 hydroxysteroid (17‐beta) dehydrogenase 2 [Source:HGNC Symbol;Acc:5211] MT‐ND5 1.272472011 ENSG00000198786 mitochondrially encoded NADH dehydrogenase 5 [Source:HGNC Symbol;Acc:7461] NNMT 1.271443298 ENSG00000166741 nicotinamide N‐methyltransferase [Source:HGNC Symbol;Acc:7861] COL21A1 1.26591797 ENSG00000124749 collagen, type XXI, alpha 1 [Source:HGNC Symbol;Acc:17025] DPYSL3 1.263257089 ENSG00000113657 dihydropyrimidinase‐like 3 [Source:HGNC Symbol;Acc:3015] C6 1.247786452 ENSG00000039537 complement component 6 [Source:HGNC Symbol;Acc:1339] ACSL1 1.242455753 ENSG00000151726 acyl‐CoA synthetase long‐chain family member 1 [Source:HGNC Symbol;Acc:3569] CDC42EP1 1.240444912 ENSG00000128283 CDC42 effector protein (Rho GTPase binding) 1 [Source:HGNC Symbol;Acc:17014] RRAD 1.237572934 ENSG00000166592 Ras‐related associated with diabetes [Source:HGNC Symbol;Acc:10446] TNFSF4 1.227743219 ENSG00000117586 tumor necrosis factor (ligand) superfamily, member 4 [Source:HGNC Symbol;Acc:11934] CAST 1.226453178 ENSG00000153113 calpastatin [Source:HGNC Symbol;Acc:1515] ADD2 1.223363823 ENSG00000075340 adducin 2 (beta) [Source:HGNC Symbol;Acc:244] STK17B 1.222495527 ENSG00000081320 serine/threonine kinase 17b [Source:HGNC Symbol;Acc:11396] CCNH 1.216465418 ENSG00000134480 cyclin H [Source:HGNC Symbol;Acc:1594] CYP24A1 1.204058663 ENSG00000019186 cytochrome P450, family 24, subfamily A, polypeptide 1 [Source:HGNC Symbol;Acc:2602] PCK2 1.198872132 ENSG00000100889 phosphoenolpyruvate carboxykinase 2 (mitochondrial) [Source:HGNC Symbol;Acc:8725] AUTS2 1.196326101 ENSG00000158321 autism susceptibility candidate 2 [Source:HGNC Symbol;Acc:14262] NEDD4 1.182062931 ENSG00000069869 neural precursor cell expressed, developmentally down‐regulated 4 [Source:HGNC Symbol;Acc:7727] EPS8 1.163828016 ENSG00000151491 epidermal growth factor receptor pathway substrate 8 [Source:HGNC Symbol;Acc:3420] CAPN2 1.159164157 ENSG00000162909 calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]

72 DNAJC6 1.148631168 ENSG00000116675 DnaJ (Hsp40) homolog, subfamily C, member 6 [Source:HGNC Symbol;Acc:15469] PDLIM1 1.143597794 ENSG00000107438 PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067] NGF 1.142516265 ENSG00000134259 nerve growth factor (beta polypeptide) [Source:HGNC Symbol;Acc:7808] MAN2A1 1.142377397 ENSG00000112893 mannosidase, alpha, class 2A, member 1 [Source:HGNC Symbol;Acc:6824] CHORDC1 1.137905836 ENSG00000110172 cysteine and histidine‐rich domain (CHORD)‐containing 1 [Source:HGNC Symbol;Acc:14525] C3orf64 1.135609025 ENSG00000163378 chromosome 3 open reading frame 64 [Source:HGNC Symbol;Acc:28526] PVRL3 1.13350923 ENSG00000177707 poliovirus receptor‐related 3 [Source:HGNC Symbol;Acc:17664] DACT1 1.131356561 ENSG00000165617 dapper, antagonist of beta‐catenin, homolog 1 (Xenopus laevis) [Source:HGNC Symbol;Acc:17748] KRT33A 1.128494711 ENSG00000006059 keratin 33A [Source:HGNC Symbol;Acc:6450] IL1A 1.127604927 ENSG00000115008 interleukin 1, alpha [Source:HGNC Symbol;Acc:5991] GATA3 1.125040453 ENSG00000107485 GATA binding protein 3 [Source:HGNC Symbol;Acc:4172] FAT4 1.124841346 ENSG00000196159 FAT tumor suppressor homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:23109] SLC22A5 1.112745412 ENSG00000197375 solute carrier family 22 (organic cation/carnitine transporter), member 5 [Source:HGNC Symbol;Acc:10969] HLX 1.112419779 ENSG00000136630 H2.0‐like homeobox [Source:HGNC Symbol;Acc:4978] DACH1 1.107175192 ENSG00000165659 dachshund homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:2663] SLCO2A1 1.099264751 ENSG00000174640 solute carrier organic anion transporter family, member 2A1 [Source:HGNC Symbol;Acc:10955] PLS3 1.098493402 ENSG00000102024 plastin 3 [Source:HGNC Symbol;Acc:9091] FBLN5 1.098211437 ENSG00000140092 fibulin 5 [Source:HGNC Symbol;Acc:3602] NR3C2 1.096074232 ENSG00000151623 nuclear receptor subfamily 3, group C, member 2 [Source:HGNC Symbol;Acc:7979] CCDC76 1.083734077 ENSG00000122435 coiled‐coil domain containing 76 [Source:HGNC Symbol;Acc:25502] CTSL2 1.08104792 ENSG00000136943 cathepsin L2 [Source:HGNC Symbol;Acc:2538] FTSJ1 1.079769709 ENSG00000068438 FtsJ homolog 1 (E. coli) [Source:HGNC Symbol;Acc:13254] MMP7 1.077710549 ENSG00000137673 matrix metallopeptidase 7 (matrilysin, uterine) [Source:HGNC Symbol;Acc:7174] TMEM43 1.07098212 ENSG00000170876 transmembrane protein 43 [Source:HGNC Symbol;Acc:28472] SLC35C1 1.069091933 ENSG00000181830 solute carrier family 35, member C1 [Source:HGNC Symbol;Acc:20197] RNF6 1.068437031 ENSG00000127870 ring finger protein (C3H2C3 type) 6 [Source:HGNC Symbol;Acc:10069] SLC2A1 1.06820776 ENSG00000117394 solute carrier family 2 (facilitated glucose transporter), member 1 [Source:HGNC Symbol;Acc:11005] SUSD5 1.064773341 ENSG00000173705 sushi domain containing 5 [Source:HGNC Symbol;Acc:29061] NRG1 1.064727629 ENSG00000157168 neuregulin 1 [Source:HGNC Symbol;Acc:7997] TTTY15 1.061122163 ENSG00000233864 testis‐specific transcript, Y‐linked 15 (non‐protein coding) [Source:HGNC Symbol;Acc:18567] AKT3 1.058800218 ENSG00000117020 v‐akt murine thymoma viral oncogene homolog 3 (protein kinase B, gamma) [Source:HGNC Symbol;Acc:393] LPIN1 1.056137303 ENSG00000134324 lipin 1 [Source:HGNC Symbol;Acc:13345] ATOX1 1.055614106 ENSG00000177556 ATX1 antioxidant protein 1 homolog (yeast) [Source:HGNC Symbol;Acc:798] STK25 1.049369688 ENSG00000115694 serine/threonine kinase 25 [Source:HGNC Symbol;Acc:11404]

73 ATP1B1 1.037313666 ENSG00000143153 ATPase, Na+/K+ transporting, beta 1 polypeptide [Source:HGNC Symbol;Acc:804] THBS1 1.037241575 ENSG00000137801 thrombospondin 1 [Source:HGNC Symbol;Acc:11785] MCTP1 1.03532876 ENSG00000175471 multiple C2 domains, transmembrane 1 [Source:HGNC Symbol;Acc:26183] FGF2 1.032596268 ENSG00000138685 fibroblast growth factor 2 (basic) [Source:HGNC Symbol;Acc:3676] C17orf91 1.026552308 ENSG00000186594 chromosome 17 open reading frame 91 [Source:HGNC Symbol;Acc:28219] HEXB 1.025319633 ENSG00000049860 hexosaminidase B (beta polypeptide) [Source:HGNC Symbol;Acc:4879] ERO1L 1.025296542 ENSG00000197930 ERO1‐like (S. cerevisiae) [Source:HGNC Symbol;Acc:13280] CNN1 1.017628001 ENSG00000130176 calponin 1, basic, smooth muscle [Source:HGNC Symbol;Acc:2155] PTPLA 1.016731427 ENSG00000165996 protein tyrosine phosphatase‐like (proline instead of catalytic arginine), member A [Source:HGNC Symbol;Acc:9639] LIPA 1.013017367 ENSG00000107798 lipase A, lysosomal acid, cholesterol esterase [Source:HGNC Symbol;Acc:6617] CTSC 1.010921799 ENSG00000109861 cathepsin C [Source:HGNC Symbol;Acc:2528] GUCY1A2 1.006740145 ENSG00000152402 guanylate cyclase 1, soluble, alpha 2 [Source:HGNC Symbol;Acc:4684] SMU1 1.00464755 ENSG00000122692 smu‐1 suppressor of mec‐8 and unc‐52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247] ANXA5 1.00454173 ENSG00000164111 annexin A5 [Source:HGNC Symbol;Acc:543] C12orf49 0.995665267 ENSG00000111412 chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128] NEAT1 0.994833551 ENSG00000245532 nuclear paraspeckle assembly transcript 1 (non‐protein coding) [Source:HGNC Symbol;Acc:30815] RRAGC 0.986694199 ENSG00000116954 Ras‐related GTP binding C [Source:HGNC Symbol;Acc:19902] LAMP2 0.986320349 ENSG00000005893 lysosomal‐associated membrane protein 2 [Source:HGNC Symbol;Acc:6501] SLCO1B3 0.983690581 ENSG00000111700 solute carrier organic anion transporter family, member 1B3 [Source:HGNC Symbol;Acc:10961] PTPRF 0.982859876 ENSG00000142949 protein tyrosine phosphatase, receptor type, F [Source:HGNC Symbol;Acc:9670] OXSR1 0.974778 ENSG00000172939 oxidative‐stress responsive 1 [Source:HGNC Symbol;Acc:8508] KIAA0020 0.971697431 ENSG00000080608 KIAA0020 [Source:HGNC Symbol;Acc:29676] CD59 0.971567611 ENSG00000085063 CD59 molecule, complement regulatory protein [Source:HGNC Symbol;Acc:1689] NT5DC3 0.964828112 ENSG00000111696 5'‐nucleotidase domain containing 3 [Source:HGNC Symbol;Acc:30826] SLC35F2 0.964049433 ENSG00000110660 solute carrier family 35, member F2 [Source:HGNC Symbol;Acc:23615] HIVEP2 0.961848362 ENSG00000010818 human immunodeficiency virus type I enhancer binding protein 2 [Source:HGNC Symbol;Acc:4921] HLA‐DRA 0.961533991 ENSG00000204287 major histocompatibility complex, class II, DR alpha [Source:HGNC Symbol;Acc:4947] MAP1B 0.959211097 ENSG00000131711 microtubule‐associated protein 1B [Source:HGNC Symbol;Acc:6836] RASAL2 0.958964889 ENSG00000075391 RAS protein activator like 2 [Source:HGNC Symbol;Acc:9874] PVR 0.958336159 ENSG00000073008 poliovirus receptor [Source:HGNC Symbol;Acc:9705] C20orf111 0.956069356 ENSG00000132823 chromosome 20 open reading frame 111 [Source:HGNC Symbol;Acc:16105] STYK1 0.955849868 ENSG00000060140 serine/threonine/tyrosine kinase 1 [Source:HGNC Symbol;Acc:18889] C12orf4 0.944883955 ENSG00000047621 chromosome 12 open reading frame 4 [Source:HGNC Symbol;Acc:1184] IL15 0.942103528 ENSG00000164136 interleukin 15 [Source:HGNC Symbol;Acc:5977]

74 ABCC1 0.939272618 ENSG00000103222 ATP‐binding cassette, sub‐family C (CFTR/MRP), member 1 [Source:HGNC Symbol;Acc:51] MMP1 0.939097561 ENSG00000196611 matrix metallopeptidase 1 (interstitial collagenase) [Source:HGNC Symbol;Acc:7155] TEX14 0.935063198 ENSG00000121101 testis expressed 14 [Source:HGNC Symbol;Acc:11737] CAPN1 0.933964734 ENSG00000014216 calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476] PLD3 0.933614228 ENSG00000105223 phospholipase D family, member 3 [Source:HGNC Symbol;Acc:17158] IGFBP4 0.927475072 ENSG00000141753 insulin‐like growth factor binding protein 4 [Source:HGNC Symbol;Acc:5473] HHLA3 0.925273209 ENSG00000197568 HERV‐H LTR‐associating 3 [Source:HGNC Symbol;Acc:4906] FSTL3 0.921909662 ENSG00000070404 follistatin‐like 3 (secreted glycoprotein) [Source:HGNC Symbol;Acc:3973] RRAS 0.921034658 ENSG00000126458 related RAS viral (r‐ras) oncogene homolog [Source:HGNC Symbol;Acc:10447] CCNA1 0.915960135 ENSG00000133101 cyclin A1 [Source:HGNC Symbol;Acc:1577] DNAJC15 0.915400396 ENSG00000120675 DnaJ (Hsp40) homolog, subfamily C, member 15 [Source:HGNC Symbol;Acc:20325] DUSP10 0.915324335 ENSG00000143507 dual specificity phosphatase 10 [Source:HGNC Symbol;Acc:3065] EDIL3 0.915263747 ENSG00000164176 EGF‐like repeats and discoidin I‐like domains 3 [Source:HGNC Symbol;Acc:3173] HLA‐DRB1 0.914905803 ENSG00000196126 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:4948] DPAGT1 0.909550463 ENSG00000172269 dolichyl‐phosphate (UDP‐N‐acetylglucosamine) N‐acetylglucosaminephosphotransferase 1 (GlcNAc‐1‐P transferase) CTSL1 0.905498639 ENSG00000135047 cathepsin L1 [Source:HGNC Symbol;Acc:2537] ESYT1 0.894158764 ENSG00000139641 extended synaptotagmin‐like protein 1 [Source:HGNC Symbol;Acc:29534] MAP7D1 0.889430284 ENSG00000116871 MAP7 domain containing 1 [Source:HGNC Symbol;Acc:25514] CTNNAL1 0.888086061 ENSG00000119326 catenin (cadherin‐associated protein), alpha‐like 1 [Source:HGNC Symbol;Acc:2512] C7orf58 0.886452103 ENSG00000106034 chromosome 7 open reading frame 58 [Source:HGNC Symbol;Acc:26159] PPFIA2 0.884394461 ENSG00000139220 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2 PRKAA1 0.882878925 ENSG00000132356 protein kinase, AMP‐activated, alpha 1 catalytic subunit [Source:HGNC Symbol;Acc:9376] NPM1 0.88166539 ENSG00000181163 nucleophosmin (nucleolar phosphoprotein B23, numatrin) [Source:HGNC Symbol;Acc:7910] GFOD1 0.879166454 ENSG00000145990 glucose‐fructose oxidoreductase domain containing 1 [Source:HGNC Symbol;Acc:21096] HOXB3 0.879111807 ENSG00000120093 homeobox B3 [Source:HGNC Symbol;Acc:5114] PPP6R1 0.874437746 ENSG00000105063 protein phosphatase 6, regulatory subunit 1 [Source:HGNC Symbol;Acc:29195] LRRFIP2 0.873526583 ENSG00000093167 leucine rich repeat (in FLII) interacting protein 2 [Source:HGNC Symbol;Acc:6703] MYC 0.872143282 ENSG00000136997 v‐myc myelocytomatosis viral oncogene homolog (avian) [Source:HGNC Symbol;Acc:7553] RETSAT 0.870182796 ENSG00000042445 retinol saturase (all‐trans‐retinol 13,14‐reductase) [Source:HGNC Symbol;Acc:25991] WNT5B 0.867206452 ENSG00000111186 wingless‐type MMTV integration site family, member 5B [Source:HGNC Symbol;Acc:16265] PPME1 0.865250294 ENSG00000214517 protein phosphatase methylesterase 1 [Source:HGNC Symbol;Acc:30178] NR3C1 0.864698956 ENSG00000113580 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) [Source:HGNC Symbol;Acc:7978] INPP1 0.859349169 ENSG00000151689 inositol polyphosphate‐1‐phosphatase [Source:HGNC Symbol;Acc:6071] ANXA4 0.85123047 ENSG00000196975 annexin A4 [Source:HGNC Symbol;Acc:542]

75 KLC2 0.849811048 ENSG00000174996 kinesin light chain 2 [Source:HGNC Symbol;Acc:20716] PPP2R3A 0.84781001 ENSG00000073711 protein phosphatase 2, regulatory subunit B'', alpha [Source:HGNC Symbol;Acc:9307] EDEM1 0.84545947 ENSG00000134109 ER degradation enhancer, mannosidase alpha‐like 1 [Source:HGNC Symbol;Acc:18967] RWDD2B 0.831854164 ENSG00000156253 RWD domain containing 2B [Source:HGNC Symbol;Acc:1302] TACC1 0.831066021 ENSG00000147526 transforming, acidic coiled‐coil containing protein 1 [Source:HGNC Symbol;Acc:11522] HPGD 0.829825579 ENSG00000164120 hydroxyprostaglandin dehydrogenase 15‐(NAD) [Source:HGNC Symbol;Acc:5154] UBE2H 0.829346112 ENSG00000186591 ubiquitin‐conjugating enzyme E2H (UBC8 homolog, yeast) [Source:HGNC Symbol;Acc:12484] CCK 0.826705688 ENSG00000187094 cholecystokinin [Source:HGNC Symbol;Acc:1569] USP25 0.823166188 ENSG00000155313 ubiquitin specific peptidase 25 [Source:HGNC Symbol;Acc:12624] DST 0.823128026 ENSG00000151914 dystonin [Source:HGNC Symbol;Acc:1090] CXCL6 0.822290235 ENSG00000124875 chemokine (C‐X‐C motif) ligand 6 (granulocyte chemotactic protein 2) [Source:HGNC Symbol;Acc:10643] PIK3CD 0.821484824 ENSG00000171608 phosphoinositide‐3‐kinase, catalytic, delta polypeptide [Source:HGNC Symbol;Acc:8977] RIC8A 0.81916624 ENSG00000177963 resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) [Source:HGNC Symbol;Acc:29550] SCRN3 0.817995401 ENSG00000144306 secernin 3 [Source:HGNC Symbol;Acc:30382] HGS 0.817678393 ENSG00000185359 hepatocyte growth factor‐regulated tyrosine kinase substrate [Source:HGNC Symbol;Acc:4897] CD3EAP 0.817248125 ENSG00000117877 CD3e molecule, epsilon associated protein [Source:HGNC Symbol;Acc:24219] AKR1B10 0.814746784 ENSG00000198074 aldo‐keto reductase family 1, member B10 (aldose reductase) [Source:HGNC Symbol;Acc:382] CALCRL 0.812807256 ENSG00000064989 calcitonin receptor‐like [Source:HGNC Symbol;Acc:16709] GBE1 0.811001893 ENSG00000114480 glucan (1,4‐alpha‐), branching enzyme 1 [Source:HGNC Symbol;Acc:4180] PLP2 0.810466475 ENSG00000102007 proteolipid protein 2 (colonic epithelium‐enriched) [Source:HGNC Symbol;Acc:9087] IFRD1 0.810097874 ENSG00000006652 interferon‐related developmental regulator 1 [Source:HGNC Symbol;Acc:5456] GARS 0.808312268 ENSG00000106105 glycyl‐tRNA synthetase [Source:HGNC Symbol;Acc:4162] BIRC2 0.807947947 ENSG00000110330 baculoviral IAP repeat‐containing 2 [Source:HGNC Symbol;Acc:590] KYNU 0.80718982 ENSG00000115919 kynureninase (L‐kynurenine hydrolase) [Source:HGNC Symbol;Acc:6469] POLB 0.807045604 ENSG00000070501 polymerase (DNA directed), beta [Source:HGNC Symbol;Acc:9174] MAPKAPK3 0.804366112 ENSG00000114738 mitogen‐activated protein kinase‐activated protein kinase 3 [Source:HGNC Symbol;Acc:6888] GRPR 0.80130575 ENSG00000126010 gastrin‐releasing peptide receptor [Source:HGNC Symbol;Acc:4609] ACD 0.798093348 ENSG00000102977 adrenocortical dysplasia homolog (mouse) [Source:HGNC Symbol;Acc:25070] MARCH1. 0.795332128 ENSG00000145416 membrane‐associated ring finger (C3HC4) 1 [Source:HGNC Symbol;Acc:26077] SP100 0.795059296 ENSG00000067066 SP100 nuclear antigen [Source:HGNC Symbol;Acc:11206] ANXA2P2 0.794599242 ENSG00000231991 annexin A2 pseudogene 2 [Source:HGNC Symbol;Acc:539] CD74 0.791874265 ENSG00000019582 CD74 molecule, major histocompatibility complex, class II invariant chain [Source:HGNC Symbol;Acc:1697] BIRC3 0.790342474 ENSG00000023445 baculoviral IAP repeat‐containing 3 [Source:HGNC Symbol;Acc:591] ITK 0.784672986 ENSG00000113263 IL2‐inducible T‐cell kinase [Source:HGNC Symbol;Acc:6171]

76 SOLH 0.781827727 ENSG00000103326 small optic lobes homolog (Drosophila) [Source:HGNC Symbol;Acc:11182] CFH 0.780313827 ENSG00000000971 complement factor H [Source:HGNC Symbol;Acc:4883] RBM19 0.779328719 ENSG00000122965 RNA binding motif protein 19 [Source:HGNC Symbol;Acc:29098] LMF2 0.776243002 ENSG00000100258 lipase maturation factor 2 [Source:HGNC Symbol;Acc:25096] C19orf10 0.775997602 ENSG00000074842 chromosome 19 open reading frame 10 [Source:HGNC Symbol;Acc:16948] DNAJC10 0.774720887 ENSG00000077232 DnaJ (Hsp40) homolog, subfamily C, member 10 [Source:HGNC Symbol;Acc:24637] RPL10 0.773174147 ENSG00000147403 ribosomal protein L10 [Source:HGNC Symbol;Acc:10298] MCAM 0.772917624 ENSG00000076706 melanoma cell adhesion molecule [Source:HGNC Symbol;Acc:6934] SFRP4 0.769581754 ENSG00000106483 secreted frizzled‐related protein 4 [Source:HGNC Symbol;Acc:10778] TRPC1 0.766626042 ENSG00000144935 transient receptor potential cation channel, subfamily C, member 1 [Source:HGNC Symbol;Acc:12333] MLPH 0.764724393 ENSG00000115648 melanophilin [Source:HGNC Symbol;Acc:29643] CUZD1 0.761054751 ENSG00000138161 CUB and zona pellucida‐like domains 1 [Source:HGNC Symbol;Acc:17937] NIP7 0.759972271 ENSG00000132603 nuclear import 7 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24328] CLDN1 0.759004619 ENSG00000163347 claudin 1 [Source:HGNC Symbol;Acc:2032] RMND1 0.758112089 ENSG00000155906 required for meiotic nuclear division 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21176] TEAD4 0.757748113 ENSG00000197905 TEA domain family member 4 [Source:HGNC Symbol;Acc:11717] LAMP1 0.756570466 ENSG00000185896 lysosomal‐associated membrane protein 1 [Source:HGNC Symbol;Acc:6499] LASS2 0.755277304 ENSG00000143418 LAG1 homolog, ceramide synthase 2 [Source:HGNC Symbol;Acc:14076] DUSP7 0.752104182 ENSG00000164086 dual specificity phosphatase 7 [Source:HGNC Symbol;Acc:3073] MAP3K5 0.750917922 ENSG00000197442 mitogen‐activated protein kinase kinase kinase 5 [Source:HGNC Symbol;Acc:6857] TMPRSS11E 0.747570219 ENSG00000087128 transmembrane protease, serine 11E [Source:HGNC Symbol;Acc:24465] DCAF17 0.74718922 ENSG00000115827 DDB1 and CUL4 associated factor 17 [Source:HGNC Symbol;Acc:25784] NPPB 0.746660524 ENSG00000120937 natriuretic peptide B [Source:HGNC Symbol;Acc:7940] HLA‐B 0.744763488 ENSG00000234745 major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:4932] SYNJ2 0.743797852 ENSG00000078269 synaptojanin 2 [Source:HGNC Symbol;Acc:11504] CYLD 0.743240173 ENSG00000083799 cylindromatosis (turban tumor syndrome) [Source:HGNC Symbol;Acc:2584] GFPT1 0.743123079 ENSG00000198380 glutamine‐‐fructose‐6‐phosphate transaminase 1 [Source:HGNC Symbol;Acc:4241] HOXB5 0.739411932 ENSG00000120075 homeobox B5 [Source:HGNC Symbol;Acc:5116] FOLR3 0.738026536 ENSG00000110203 folate receptor 3 (gamma) [Source:HGNC Symbol;Acc:3795] NAT9 0.737841556 ENSG00000109065 N‐acetyltransferase 9 (GCN5‐related, putative) [Source:HGNC Symbol;Acc:23133] CDK9 0.733144382 ENSG00000136807 cyclin‐dependent kinase 9 [Source:HGNC Symbol;Acc:1780] DDX47 0.732183719 ENSG00000213782 DEAD (Asp‐Glu‐Ala‐Asp) box polypeptide 47 [Source:HGNC Symbol;Acc:18682] MSTN 0.729849713 ENSG00000138379 myostatin [Source:HGNC Symbol;Acc:4223] CLTB 0.729736045 ENSG00000175416 clathrin, light chain B [Source:HGNC Symbol;Acc:2091]

77 MMP3 0.728485372 ENSG00000149968 matrix metallopeptidase 3 (stromelysin 1, progelatinase) [Source:HGNC Symbol;Acc:7173] UQCC 0.726362908 ENSG00000101019 ubiquinol‐cytochrome c reductase complex chaperone [Source:HGNC Symbol;Acc:15891] CDH4 0.724702915 ENSG00000179242 cadherin 4, type 1, R‐cadherin (retinal) [Source:HGNC Symbol;Acc:1763] WDR33 0.720995022 ENSG00000136709 WD repeat domain 33 [Source:HGNC Symbol;Acc:25651] CDCA4 0.718401356 ENSG00000170779 cell division cycle associated 4 [Source:HGNC Symbol;Acc:14625] UBE2Z 0.717381562 ENSG00000159202 ubiquitin‐conjugating enzyme E2Z [Source:HGNC Symbol;Acc:25847] TUBB6 0.716133144 ENSG00000176014 tubulin, beta 6 [Source:HGNC Symbol;Acc:20776] RBMS3 0.711965196 ENSG00000144642 RNA binding motif, single stranded interacting protein 3 [Source:HGNC Symbol;Acc:13427] VASP 0.711149529 ENSG00000125753 vasodilator‐stimulated phosphoprotein [Source:HGNC Symbol;Acc:12652] RPL37A 0.708384409 ENSG00000197756 ribosomal protein L37a [Source:HGNC Symbol;Acc:10348] ERCC6 0.708221618 ENSG00000225830 excision repair cross‐complementing rodent repair deficiency, complementation group 6 ARF4 0.701412584 ENSG00000168374 ADP‐ribosylation factor 4 [Source:HGNC Symbol;Acc:655] RBM7 0.700650875 ENSG00000076053 RNA binding motif protein 7 [Source:HGNC Symbol;Acc:9904] LUZP1 0.695543244 ENSG00000169641 leucine zipper protein 1 [Source:HGNC Symbol;Acc:14985] EXT2 0.690074784 ENSG00000151348 exostosin 2 [Source:HGNC Symbol;Acc:3513] ANKRD28 0.687206318 ENSG00000206560 ankyrin repeat domain 28 [Source:HGNC Symbol;Acc:29024] HMOX2 0.686556158 ENSG00000103415 heme oxygenase (decycling) 2 [Source:HGNC Symbol;Acc:5014] AR 0.686467795 ENSG00000169083 androgen receptor [Source:HGNC Symbol;Acc:644] UVRAG 0.685258561 ENSG00000198382 UV radiation resistance associated gene [Source:HGNC Symbol;Acc:12640] ITPR3 0.682478892 ENSG00000096433 inositol 1,4,5‐triphosphate receptor, type 3 [Source:HGNC Symbol;Acc:6182] LGALS3BP 0.67998934 ENSG00000108679 lectin, galactoside‐binding, soluble, 3 binding protein [Source:HGNC Symbol;Acc:6564] TRAM2 0.678532793 ENSG00000065308 translocation associated membrane protein 2 [Source:HGNC Symbol;Acc:16855] CREB3 0.678482313 ENSG00000107175 cAMP responsive element binding protein 3 [Source:HGNC Symbol;Acc:2347] PPPDE2 0.678001809 ENSG00000100418 PPPDE peptidase domain containing 2 [Source:HGNC Symbol;Acc:24577] SGCE 0.677616564 ENSG00000127990 sarcoglycan, epsilon [Source:HGNC Symbol;Acc:10808] CES3 0.673801452 ENSG00000172828 carboxylesterase 3 [Source:HGNC Symbol;Acc:1865] FKBP14 0.673257571 ENSG00000106080 FK506 binding protein 14, 22 kDa [Source:HGNC Symbol;Acc:18625] CD163 0.672718268 ENSG00000177575 CD163 molecule [Source:HGNC Symbol;Acc:1631] TBC1D8B 0.67046169 ENSG00000133138 TBC1 domain family, member 8B (with GRAM domain) [Source:HGNC Symbol;Acc:24715] PKMYT1 0.666458747 ENSG00000127564 protein kinase, membrane associated tyrosine/threonine 1 [Source:HGNC Symbol;Acc:29650] ATP6V1D 0.666351205 ENSG00000100554 ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D [Source:HGNC Symbol;Acc:13527] CYTIP 0.665179066 ENSG00000115165 cytohesin 1 interacting protein [Source:HGNC Symbol;Acc:9506] TFCP2L1 0.665018179 ENSG00000115112 transcription factor CP2‐like 1 [Source:HGNC Symbol;Acc:17925] CD151 0.663917719 ENSG00000177697 CD151 molecule (Raph blood group) [Source:HGNC Symbol;Acc:1630]

78 ACSL4 0.661700006 ENSG00000068366 acyl‐CoA synthetase long‐chain family member 4 [Source:HGNC Symbol;Acc:3571] RUNX1T1 0.661700006 ENSG00000079102 runt‐related transcription factor 1; translocated to, 1 (cyclin D‐related) [Source:HGNC Symbol;Acc:1535] BIN1 0.658617319 ENSG00000136717 bridging integrator 1 [Source:HGNC Symbol;Acc:1052] LEF1 0.658191394 ENSG00000138795 lymphoid enhancer‐binding factor 1 [Source:HGNC Symbol;Acc:6551] POLR3G 0.657482666 ENSG00000113356 polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075] MICAL2 0.654468192 ENSG00000133816 microtubule associated monoxygenase, calponin and LIM domain containing 2 [Source:HGNC Symbol;Acc:24693] CCDC6 0.653747753 ENSG00000108091 coiled‐coil domain containing 6 [Source:HGNC Symbol;Acc:18782] WARS 0.650401706 ENSG00000140105 tryptophanyl‐tRNA synthetase [Source:HGNC Symbol;Acc:12729] SLC2A6 0.64827622 ENSG00000160326 solute carrier family 2 (facilitated glucose transporter), member 6 [Source:HGNC Symbol;Acc:11011] GMPPB 0.639459257 ENSG00000173540 GDP‐mannose pyrophosphorylase B [Source:HGNC Symbol;Acc:22932] MMP10 0.637259055 ENSG00000166670 matrix metallopeptidase 10 (stromelysin 2) [Source:HGNC Symbol;Acc:7156] FNBP1L 0.634955462 ENSG00000137942 formin binding protein 1‐like [Source:HGNC Symbol;Acc:20851] ADRA1D 0.63378215 ENSG00000171873 adrenergic, alpha‐1D‐, receptor [Source:HGNC Symbol;Acc:280] DAP 0.632603378 ENSG00000112977 death‐associated protein [Source:HGNC Symbol;Acc:2672] COL4A6 0.632154555 ENSG00000197565 collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:2208] LGTN 0.630565436 ENSG00000143486 ligatin [Source:HGNC Symbol;Acc:6583] UXS1 0.627243696 ENSG00000115652 UDP‐glucuronate decarboxylase 1 [Source:HGNC Symbol;Acc:17729] PUS1 0.626938654 ENSG00000177192 pseudouridylate synthase 1 [Source:HGNC Symbol;Acc:15508] PDCD1LG2 0.626707154 ENSG00000197646 programmed cell death 1 ligand 2 [Source:HGNC Symbol;Acc:18731] RUNX1 0.626390924 ENSG00000159216 runt‐related transcription factor 1 [Source:HGNC Symbol;Acc:10471] MYL12B 0.625901192 ENSG00000118680 myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827] PLEKHB2 0.624358977 ENSG00000115762 pleckstrin homology domain containing, family B (evectins) member 2 [Source:HGNC Symbol;Acc:19236] SSSCA1 0.623647327 ENSG00000173465 Sjogren syndrome/scleroderma autoantigen 1 [Source:HGNC Symbol;Acc:11328] SDCCAG8 0.623473318 ENSG00000054282 serologically defined colon cancer antigen 8 [Source:HGNC Symbol;Acc:10671] KIRREL 0.620554739 ENSG00000183853 kin of IRRE like (Drosophila) [Source:HGNC Symbol;Acc:15734] SETD3 0.620472245 ENSG00000183576 SET domain containing 3 [Source:HGNC Symbol;Acc:20493] PHKB 0.61973952 ENSG00000102893 phosphorylase kinase, beta [Source:HGNC Symbol;Acc:8927] RARS 0.618756737 ENSG00000113643 arginyl‐tRNA synthetase [Source:HGNC Symbol;Acc:9870] ERBB2IP 0.617316785 ENSG00000112851 erbb2 interacting protein [Source:HGNC Symbol;Acc:15842] GTF3C3 0.617169859 ENSG00000119041 general transcription factor IIIC, polypeptide 3, 102kDa [Source:HGNC Symbol;Acc:4666] ITGB2 0.616952536 ENSG00000160255 integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) [Source:HGNC Symbol;Acc:6155] GIT2 0.614809576 ENSG00000139436 G protein‐coupled receptor kinase interacting ArfGAP 2 [Source:HGNC Symbol;Acc:4273] DOCK9 0.6118641 ENSG00000088387 dedicator of cytokinesis 9 [Source:HGNC Symbol;Acc:14132] FBXL6 0.610686286 ENSG00000182325 F‐box and leucine‐rich repeat protein 6 [Source:HGNC Symbol;Acc:13603]

79 RAD54L2 0.609165704 ENSG00000164080 RAD54‐like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:29123] TRMT1 0.609084039 ENSG00000104907 TRM1 tRNA methyltransferase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25980] COL7A1 0.608024986 ENSG00000114270 collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214] USP15 0.603551406 ENSG00000135655 ubiquitin specific peptidase 15 [Source:HGNC Symbol;Acc:12613] ANKMY2 0.602713776 ENSG00000106524 ankyrin repeat and MYND domain containing 2 [Source:HGNC Symbol;Acc:25370] C2orf49 0.600769834 ENSG00000135974 chromosome 2 open reading frame 49 [Source:HGNC Symbol;Acc:28772]

80 Supp Table S3B: Genes downregulated by 4SA by 1.5 fold or lower

Gene symbol 4SAminV Ensembl ID Description Column2 Column3 Column4 Column5 Column6 SOBP ‐5.008017418 ENSG00000112320 sine oculis binding protein homolog (Drosophila) [Source:HGNC Symbol;Acc:29256] TNFAIP6 ‐4.278596632 ENSG00000123610 tumor necrosis factor, alpha‐induced protein 6 [Source:HGNC Symbol;Acc:11898] TTYH1 ‐3.983817006 ENSG00000167614 tweety homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:13476] S100B ‐3.836334137 ENSG00000160307 S100 calcium binding protein B [Source:HGNC Symbol;Acc:10500] PTPRZ1 ‐3.304344916 ENSG00000106278 protein tyrosine phosphatase, receptor‐type, Z polypeptide 1 [Source:HGNC Symbol;Acc:9685] ABAT ‐3.278168244 ENSG00000183044 4‐aminobutyrate aminotransferase [Source:HGNC Symbol;Acc:23] MLC1 ‐3.271030668 ENSG00000100427 megalencephalic leukoencephalopathy with subcortical cysts 1 [Source:HGNC Symbol;Acc:17082] CSGALNACT1 ‐3.231484611 ENSG00000147408 chondroitin sulfate N‐acetylgalactosaminyltransferase 1 [Source:HGNC Symbol;Acc:24290] PSD3 ‐2.880372654 ENSG00000156011 pleckstrin and Sec7 domain containing 3 [Source:HGNC Symbol;Acc:19093] ST3GAL5 ‐2.796270792 ENSG00000115525 ST3 beta‐galactoside alpha‐2,3‐sialyltransferase 5 [Source:HGNC Symbol;Acc:10872] HEY1 ‐2.742087118 ENSG00000164683 hairy/enhancer‐of‐split related with YRPW motif 1 [Source:HGNC Symbol;Acc:4880] SALL1 ‐2.694360827 ENSG00000103449 sal‐like 1 (Drosophila) [Source:HGNC Symbol;Acc:10524] SOX11 ‐2.610875031 ENSG00000176887 SRY (sex determining region Y)‐box 11 [Source:HGNC Symbol;Acc:11191] CHD7 ‐2.514182437 ENSG00000171316 chromodomain helicase DNA binding protein 7 [Source:HGNC Symbol;Acc:20626] DUSP6 ‐2.503051337 ENSG00000139318 dual specificity phosphatase 6 [Source:HGNC Symbol;Acc:3072] ID2 ‐2.500034219 ENSG00000115738 inhibitor of DNA binding 2, dominant negative helix‐loop‐helix protein [Source:HGNC Symbol;Acc:5361] PTN ‐2.378417216 ENSG00000105894 pleiotrophin [Source:HGNC Symbol;Acc:9630] SOX9 ‐2.341882953 ENSG00000125398 SRY (sex determining region Y)‐box 9 [Source:HGNC Symbol;Acc:11204] SLC47A1 ‐2.302173483 ENSG00000142494 solute carrier family 47, member 1 [Source:HGNC Symbol;Acc:25588] ID1 ‐2.279798621 ENSG00000125968 inhibitor of DNA binding 1, dominant negative helix‐loop‐helix protein [Source:HGNC Symbol;Acc:5360] VASH1 ‐2.269155865 ENSG00000071246 vasohibin 1 [Source:HGNC Symbol;Acc:19964] TRIM9 ‐2.260326329 ENSG00000100505 tripartite motif‐containing 9 [Source:HGNC Symbol;Acc:16288] B3GAT1 ‐2.248385404 ENSG00000109956 beta‐1,3‐glucuronyltransferase 1 (glucuronosyltransferase P) [Source:HGNC Symbol;Acc:921] SDC3 ‐2.221692574 ENSG00000162512 syndecan 3 [Source:HGNC Symbol;Acc:10660] CCND2 ‐2.189212966 ENSG00000118971 cyclin D2 [Source:HGNC Symbol;Acc:1583] PALM ‐2.180420026 ENSG00000099864 paralemmin [Source:HGNC Symbol;Acc:8594] NXN ‐2.178867775 ENSG00000167693 nucleoredoxin [Source:HGNC Symbol;Acc:18008] SNX10 ‐2.160379216 ENSG00000086300 sorting nexin 10 [Source:HGNC Symbol;Acc:14974] HOPX ‐2.149792561 ENSG00000171476 HOP homeobox [Source:HGNC Symbol;Acc:24961] EEF1A2 ‐2.120101312 ENSG00000101210 eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192] GPM6B ‐2.107963189 ENSG00000046653 glycoprotein M6B [Source:HGNC Symbol;Acc:4461]

81 KCTD12 ‐2.066604241 ENSG00000178695 potassium channel tetramerisation domain containing 12 [Source:HGNC Symbol;Acc:14678] LTBP1 ‐2.020229141 ENSG00000049323 latent transforming growth factor beta binding protein 1 [Source:HGNC Symbol;Acc:6714] FABP7 ‐1.998943638 ENSG00000164434 fatty acid binding protein 7, brain [Source:HGNC Symbol;Acc:3562] IQGAP2 ‐1.994115027 ENSG00000145703 IQ motif containing GTPase activating protein 2 [Source:HGNC Symbol;Acc:6111] TRIB2 ‐1.987116459 ENSG00000071575 tribbles homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:30809] REV3L ‐1.978137111 ENSG00000009413 REV3‐like, catalytic subunit of DNA polymerase zeta (yeast) [Source:HGNC Symbol;Acc:9968] BCL7A ‐1.885822821 ENSG00000110987 B‐cell CLL/lymphoma 7A [Source:HGNC Symbol;Acc:1004] PPP2R2B ‐1.828422357 ENSG00000156475 protein phosphatase 2, regulatory subunit B, beta [Source:HGNC Symbol;Acc:9305] PTPN13 ‐1.821938681 ENSG00000163629 protein tyrosine phosphatase, non‐receptor type 13 (APO‐1/CD95 (Fas)‐associated phosphatase) [Source:HGNC Symbol;Acc:9646] GLUL ‐1.767727154 ENSG00000135821 glutamate‐ammonia ligase [Source:HGNC Symbol;Acc:4341] TCF12 ‐1.749046077 ENSG00000140262 transcription factor 12 [Source:HGNC Symbol;Acc:11623] PDPN ‐1.737401243 ENSG00000162493 podoplanin [Source:HGNC Symbol;Acc:29602] FXYD6 ‐1.720986816 ENSG00000137726 FXYD domain containing ion transport regulator 6 [Source:HGNC Symbol;Acc:4030] PIK3C2B ‐1.698717047 ENSG00000133056 phosphoinositide‐3‐kinase, class 2, beta polypeptide [Source:HGNC Symbol;Acc:8972] APBB2 ‐1.691410363 ENSG00000163697 amyloid beta (A4) precursor protein‐binding, family B, member 2 [Source:HGNC Symbol;Acc:582] LASS6 ‐1.685372432 ENSG00000172292 LAG1 homolog, ceramide synthase 6 [Source:HGNC Symbol;Acc:23826] MYO10 ‐1.684787917 ENSG00000145555 myosin X [Source:HGNC Symbol;Acc:7593] TRIM24 ‐1.643019842 ENSG00000122779 tripartite motif‐containing 24 [Source:HGNC Symbol;Acc:11812] HTRA1 ‐1.641839415 ENSG00000166033 HtrA serine peptidase 1 [Source:HGNC Symbol;Acc:9476] NELL2 ‐1.617170976 ENSG00000184613 NEL‐like 2 (chicken) [Source:HGNC Symbol;Acc:7751] GRIK1 ‐1.611016804 ENSG00000171189 glutamate receptor, ionotropic, kainate 1 [Source:HGNC Symbol;Acc:4579] DAAM1 ‐1.597535416 ENSG00000100592 dishevelled associated activator of morphogenesis 1 [Source:HGNC Symbol;Acc:18142] RLBP1 ‐1.573948537 ENSG00000140522 retinaldehyde binding protein 1 [Source:HGNC Symbol;Acc:10024] SEP6. ‐1.558164605 ENSG00000125354 septin 6 [Source:HGNC Symbol;Acc:15848] SFRP1 ‐1.552762745 ENSG00000104332 secreted frizzled‐related protein 1 [Source:HGNC Symbol;Acc:10776] TRPS1 ‐1.546221954 ENSG00000104447 trichorhinophalangeal syndrome I [Source:HGNC Symbol;Acc:12340] CREB5 ‐1.526253854 ENSG00000146592 cAMP responsive element binding protein 5 [Source:HGNC Symbol;Acc:16844] ITPKB ‐1.520200763 ENSG00000143772 inositol 1,4,5‐trisphosphate 3‐kinase B [Source:HGNC Symbol;Acc:6179] SASH1 ‐1.517382804 ENSG00000111961 SAM and SH3 domain containing 1 [Source:HGNC Symbol;Acc:19182] COL4A1 ‐1.507834587 ENSG00000187498 collagen, type IV, alpha 1 [Source:HGNC Symbol;Acc:2202] SALL2 ‐1.507455731 ENSG00000165821 sal‐like 2 (Drosophila) [Source:HGNC Symbol;Acc:10526] CASP7 ‐1.504917998 ENSG00000165806 caspase 7, apoptosis‐related cysteine peptidase [Source:HGNC Symbol;Acc:1508] INHBB ‐1.48769379 ENSG00000163083 inhibin, beta B [Source:HGNC Symbol;Acc:6067] ARNT2 ‐1.473259011 ENSG00000172379 aryl‐hydrocarbon receptor nuclear translocator 2 [Source:HGNC Symbol;Acc:16876] MAPK10 ‐1.460410849 ENSG00000109339 mitogen‐activated protein kinase 10 [Source:HGNC Symbol;Acc:6872]

82 PPM1D ‐1.424441172 ENSG00000170836 protein phosphatase, Mg2+/Mn2+ dependent, 1D [Source:HGNC Symbol;Acc:9277] SHROOM2 ‐1.424270126 ENSG00000146950 shroom family member 2 [Source:HGNC Symbol;Acc:630] LRRN2 ‐1.411021407 ENSG00000170382 leucine rich repeat neuronal 2 [Source:HGNC Symbol;Acc:16914] SV2A ‐1.410229793 ENSG00000159164 synaptic vesicle glycoprotein 2A [Source:HGNC Symbol;Acc:20566] PPFIBP2 ‐1.407269803 ENSG00000166387 PTPRF interacting protein, binding protein 2 (liprin beta 2) [Source:HGNC Symbol;Acc:9250] KCNJ16 ‐1.361063507 ENSG00000153822 potassium inwardly‐rectifying channel, subfamily J, member 16 [Source:HGNC Symbol;Acc:6262] TCF4 ‐1.348924388 ENSG00000196628 transcription factor 4 [Source:HGNC Symbol;Acc:11634] NKX2‐2 ‐1.337422139 ENSG00000125820 NK2 homeobox 2 [Source:HGNC Symbol;Acc:7835] MGAT4A ‐1.327872965 ENSG00000071073 mannosyl (alpha‐1,3‐)‐glycoprotein beta‐1,4‐N‐acetylglucosaminyltransferase, isozyme A [Source:HGNC Symbol;Acc:7047] PELI2 ‐1.325925674 ENSG00000139946 pellino homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:8828] ALDH3A2 ‐1.313926384 ENSG00000072210 aldehyde dehydrogenase 3 family, member A2 [Source:HGNC Symbol;Acc:403] GABBR2 ‐1.307452131 ENSG00000136928 gamma‐aminobutyric acid (GABA) B receptor, 2 [Source:HGNC Symbol;Acc:4507] RAB33A ‐1.305377378 ENSG00000134594 RAB33A, member RAS oncogene family [Source:HGNC Symbol;Acc:9773] RND2 ‐1.287585432 ENSG00000108830 Rho family GTPase 2 [Source:HGNC Symbol;Acc:18315] EAF2 ‐1.265061541 ENSG00000145088 ELL associated factor 2 [Source:HGNC Symbol;Acc:23115] NEO1 ‐1.263559691 ENSG00000067141 neogenin 1 [Source:HGNC Symbol;Acc:7754] SEMA6D ‐1.263449679 ENSG00000137872 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770] PRCP ‐1.239909716 ENSG00000137509 prolylcarboxypeptidase (angiotensinase C) [Source:HGNC Symbol;Acc:9344] SEZ6L ‐1.237347432 ENSG00000100095 seizure related 6 homolog (mouse)‐like [Source:HGNC Symbol;Acc:10763] FBXL7 ‐1.230936329 ENSG00000183580 F‐box and leucine‐rich repeat protein 7 [Source:HGNC Symbol;Acc:13604] METTL7A ‐1.220842962 ENSG00000185432 methyltransferase like 7A [Source:HGNC Symbol;Acc:24550] ROBLD3 ‐1.216704819 ENSG00000116586 roadblock domain containing 3 [Source:HGNC Symbol;Acc:29796] TRAPPC6A ‐1.210237225 ENSG00000007255 trafficking protein particle complex 6A [Source:HGNC Symbol;Acc:23069] TMEM121 ‐1.205371475 ENSG00000184986 transmembrane protein 121 [Source:HGNC Symbol;Acc:20511] PKIG ‐1.201839844 ENSG00000168734 protein kinase (cAMP‐dependent, catalytic) inhibitor gamma [Source:HGNC Symbol;Acc:9019] SNN ‐1.193384699 ENSG00000184602 stannin [Source:HGNC Symbol;Acc:11149] SCAMP5 ‐1.182095669 ENSG00000198794 secretory carrier membrane protein 5 [Source:HGNC Symbol;Acc:30386] TP53TG1 ‐1.169367667 ENSG00000182165 TP53 target 1 (non‐protein coding) [Source:HGNC Symbol;Acc:17026] SUV420H1 ‐1.161192497 ENSG00000110066 suppressor of variegation 4‐20 homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:24283] CORO2B ‐1.14543111 ENSG00000103647 coronin, actin binding protein, 2B [Source:HGNC Symbol;Acc:2256] KAT2B ‐1.133522289 ENSG00000114166 K(lysine) acetyltransferase 2B [Source:HGNC Symbol;Acc:8638] PBX1 ‐1.130346073 ENSG00000185630 pre‐B‐cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632] RALGAPA1 ‐1.128839627 ENSG00000174373 Ral GTPase activating protein, alpha subunit 1 (catalytic) [Source:HGNC Symbol;Acc:17770] PTK2 ‐1.128398111 ENSG00000169398 PTK2 protein tyrosine kinase 2 [Source:HGNC Symbol;Acc:9611] TSPAN3 ‐1.120387679 ENSG00000140391 tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

83 BTBD3 ‐1.118948234 ENSG00000132640 BTB (POZ) domain containing 3 [Source:HGNC Symbol;Acc:15854] TCEA2 ‐1.114837671 ENSG00000171703 transcription elongation factor A (SII), 2 [Source:HGNC Symbol;Acc:11614] MAP2K5 ‐1.10050971 ENSG00000137764 mitogen‐activated protein kinase kinase 5 [Source:HGNC Symbol;Acc:6845] EXTL3 ‐1.090532133 ENSG00000012232 exostoses (multiple)‐like 3 [Source:HGNC Symbol;Acc:3518] NLGN4Y ‐1.089688443 ENSG00000165246 neuroligin 4, Y‐linked [Source:HGNC Symbol;Acc:15529] ISYNA1 ‐1.085444903 ENSG00000105655 inositol‐3‐phosphate synthase 1 [Source:HGNC Symbol;Acc:29821] GPRC5C ‐1.073974065 ENSG00000170412 G protein‐coupled receptor, family C, group 5, member C [Source:HGNC Symbol;Acc:13309] PDCD4 ‐1.072553987 ENSG00000150593 programmed cell death 4 (neoplastic transformation inhibitor) [Source:HGNC Symbol;Acc:8763] HLF ‐1.061223217 ENSG00000108924 hepatic leukemia factor [Source:HGNC Symbol;Acc:4977] SESN1 ‐1.050938185 ENSG00000080546 sestrin 1 [Source:HGNC Symbol;Acc:21595] GTDC1 ‐1.045955212 ENSG00000121964 glycosyltransferase‐like domain containing 1 [Source:HGNC Symbol;Acc:20887] MREG ‐1.034893721 ENSG00000118242 melanoregulin [Source:HGNC Symbol;Acc:25478] ATAD2B ‐1.029474924 ENSG00000119778 ATPase family, AAA domain containing 2B [Source:HGNC Symbol;Acc:29230] PTPRN2 ‐1.029342185 ENSG00000155093 protein tyrosine phosphatase, receptor type, N polypeptide 2 [Source:HGNC Symbol;Acc:9677] KCTD15 ‐1.023735898 ENSG00000153885 potassium channel tetramerisation domain containing 15 [Source:HGNC Symbol;Acc:23297] SSBP2 ‐1.017847278 ENSG00000145687 single‐stranded DNA binding protein 2 [Source:HGNC Symbol;Acc:15831] COX16 ‐1.017106835 ENSG00000133983 COX16 cytochrome c oxidase assembly homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20213] KPNA1 ‐1.010421822 ENSG00000114030 karyopherin alpha 1 (importin alpha 5) [Source:HGNC Symbol;Acc:6394] FAM117A ‐1.002641995 ENSG00000121104 family with sequence similarity 117, member A [Source:HGNC Symbol;Acc:24179] GGPS1 ‐0.997658315 ENSG00000152904 geranylgeranyl diphosphate synthase 1 [Source:HGNC Symbol;Acc:4249] ADAM23 ‐0.997214227 ENSG00000114948 ADAM metallopeptidase domain 23 [Source:HGNC Symbol;Acc:202] RAMP2 ‐0.994140163 ENSG00000131477 receptor (G protein‐coupled) activity modifying protein 2 [Source:HGNC Symbol;Acc:9844] ACYP2 ‐0.99222211 ENSG00000170634 acylphosphatase 2, muscle type [Source:HGNC Symbol;Acc:180] TOP2B ‐0.988770179 ENSG00000077097 topoisomerase (DNA) II beta 180kDa [Source:HGNC Symbol;Acc:11990] TRAF3IP2 ‐0.983088082 ENSG00000056972 TRAF3 interacting protein 2 [Source:HGNC Symbol;Acc:1343] ZNF184 ‐0.975701379 ENSG00000096654 zinc finger protein 184 [Source:HGNC Symbol;Acc:12975] BTG2 ‐0.970723429 ENSG00000159388 BTG family, member 2 [Source:HGNC Symbol;Acc:1131] TMEM158 ‐0.965750503 ENSG00000249992 transmembrane protein 158 (gene/pseudogene) [Source:HGNC Symbol;Acc:30293] LEPROTL1 ‐0.957536489 ENSG00000104660 leptin receptor overlapping transcript‐like 1 [Source:HGNC Symbol;Acc:6555] GYG2 ‐0.949728408 ENSG00000056998 glycogenin 2 [Source:HGNC Symbol;Acc:4700] BLOC1S1 ‐0.945679607 ENSG00000135441 biogenesis of lysosomal organelles complex‐1, subunit 1 [Source:HGNC Symbol;Acc:4200] CD200 ‐0.939373132 ENSG00000091972 CD200 molecule [Source:HGNC Symbol;Acc:7203] DBI ‐0.93756834 ENSG00000155368 diazepam binding inhibitor (GABA receptor modulator, acyl‐CoA binding protein) [Source:HGNC Symbol;Acc:2690] FYN ‐0.935918361 ENSG00000010810 FYN oncogene related to SRC, FGR, YES [Source:HGNC Symbol;Acc:4037] GNAZ ‐0.935141018 ENSG00000128266 guanine nucleotide binding protein (G protein), alpha z polypeptide [Source:HGNC Symbol;Acc:4395]

84 MERTK ‐0.927218233 ENSG00000153208 c‐mer proto‐oncogene tyrosine kinase [Source:HGNC Symbol;Acc:7027] SRR ‐0.925751885 ENSG00000167720 serine racemase [Source:HGNC Symbol;Acc:14398] MXD4 ‐0.925194184 ENSG00000123933 MAX dimerization protein 4 [Source:HGNC Symbol;Acc:13906] ADAM19 ‐0.920560577 ENSG00000135074 ADAM metallopeptidase domain 19 [Source:HGNC Symbol;Acc:197] STK38L ‐0.911197852 ENSG00000211455 serine/threonine kinase 38 like [Source:HGNC Symbol;Acc:17848] AASS ‐0.911057828 ENSG00000008311 aminoadipate‐semialdehyde synthase [Source:HGNC Symbol;Acc:17366] KPTN ‐0.900691149 ENSG00000118162 kaptin (actin binding protein) [Source:HGNC Symbol;Acc:6404] WIPF1 ‐0.899010529 ENSG00000115935 WAS/WASL interacting protein family, member 1 [Source:HGNC Symbol;Acc:12736] SEMA5A ‐0.893724956 ENSG00000112902 sema domain, seven thrombospondin repeats (type 1 and type 1‐like), transmembrane domain (TM) and short cytoplasmic domain, ( SP4 ‐0.893076525 ENSG00000105866 Sp4 transcription factor [Source:HGNC Symbol;Acc:11209] ITGA10 ‐0.892804572 ENSG00000143127 integrin, alpha 10 [Source:HGNC Symbol;Acc:6135] SIPA1L1 ‐0.891154193 ENSG00000197555 signal‐induced proliferation‐associated 1 like 1 [Source:HGNC Symbol;Acc:20284] DNALI1 ‐0.884957532 ENSG00000163879 dynein, axonemal, light intermediate chain 1 [Source:HGNC Symbol;Acc:14353] RARRES3 ‐0.884402259 ENSG00000133321 retinoic acid receptor responder (tazarotene induced) 3 [Source:HGNC Symbol;Acc:9869] ISG15 ‐0.882867057 ENSG00000187608 ISG15 ubiquitin‐like modifier [Source:HGNC Symbol;Acc:4053] GOLM1 ‐0.879082748 ENSG00000135052 golgi membrane protein 1 [Source:HGNC Symbol;Acc:15451] THYN1 ‐0.875663448 ENSG00000151500 thymocyte nuclear protein 1 [Source:HGNC Symbol;Acc:29560] BACH2 ‐0.874642097 ENSG00000112182 BTB and CNC homology 1, basic leucine zipper transcription factor 2 [Source:HGNC Symbol;Acc:14078] SEP9. ‐0.869284187 ENSG00000184640 septin 9 [Source:HGNC Symbol;Acc:7323] CKB ‐0.86360096 ENSG00000166165 creatine kinase, brain [Source:HGNC Symbol;Acc:1991] BCAN ‐0.86272158 ENSG00000132692 brevican [Source:HGNC Symbol;Acc:23059] CELSR2 ‐0.856303037 ENSG00000143126 cadherin, EGF LAG seven‐pass G‐type receptor 2 (flamingo homolog, Drosophila) [Source:HGNC Symbol;Acc:3231] PJA1 ‐0.852463047 ENSG00000181191 praja ring finger 1 [Source:HGNC Symbol;Acc:16648] SNRNP35 ‐0.852050939 ENSG00000184209 small nuclear ribonucleoprotein 35kDa (U11/U12) [Source:HGNC Symbol;Acc:30852] PYY ‐0.84501281 ENSG00000131096 peptide YY [Source:HGNC Symbol;Acc:9748] ZIC1 ‐0.844513207 ENSG00000152977 Zic family member 1 (odd‐paired homolog, Drosophila) [Source:HGNC Symbol;Acc:12872] VAMP8 ‐0.844194616 ENSG00000118640 vesicle‐associated membrane protein 8 (endobrevin) [Source:HGNC Symbol;Acc:12647] MAMLD1 ‐0.84376952 ENSG00000013619 mastermind‐like domain containing 1 [Source:HGNC Symbol;Acc:2568] PCBP4 ‐0.84298598 ENSG00000090097 poly(rC) binding protein 4 [Source:HGNC Symbol;Acc:8652] CNNM3 ‐0.841074411 ENSG00000168763 cyclin M3 [Source:HGNC Symbol;Acc:104] ABCA5 ‐0.835581998 ENSG00000154265 ATP‐binding cassette, sub‐family A (ABC1), member 5 [Source:HGNC Symbol;Acc:35] HMBOX1 ‐0.833536077 ENSG00000147421 homeobox containing 1 [Source:HGNC Symbol;Acc:26137] ATP9B ‐0.830326589 ENSG00000166377 ATPase, class II, type 9B [Source:HGNC Symbol;Acc:13541] DAPK1 ‐0.824471053 ENSG00000196730 death‐associated protein kinase 1 [Source:HGNC Symbol;Acc:2674] MARCKSL1 ‐0.822177217 ENSG00000175130 MARCKS‐like 1 [Source:HGNC Symbol;Acc:7142]

85 RFX5 ‐0.811496004 ENSG00000143390 regulatory factor X, 5 (influences HLA class II expression) [Source:HGNC Symbol;Acc:9986] DNAJC22 ‐0.809716534 ENSG00000178401 DnaJ (Hsp40) homolog, subfamily C, member 22 [Source:HGNC Symbol;Acc:25802] DUSP2 ‐0.809473084 ENSG00000158050 dual specificity phosphatase 2 [Source:HGNC Symbol;Acc:3068] COG7 ‐0.807626465 ENSG00000168434 component of oligomeric golgi complex 7 [Source:HGNC Symbol;Acc:18622] PC ‐0.804340411 ENSG00000173599 pyruvate carboxylase [Source:HGNC Symbol;Acc:8636] TTC3P1 ‐0.801527808 ENSG00000215105 tetratricopeptide repeat domain 3 pseudogene 1 [Source:HGNC Symbol;Acc:23318] CDC42EP4 ‐0.799647837 ENSG00000179604 CDC42 effector protein (Rho GTPase binding) 4 [Source:HGNC Symbol;Acc:17147] ADAM22 ‐0.798630931 ENSG00000008277 ADAM metallopeptidase domain 22 [Source:HGNC Symbol;Acc:201] ATP9A ‐0.795818921 ENSG00000054793 ATPase, class II, type 9A [Source:HGNC Symbol;Acc:13540] ING4 ‐0.794681987 ENSG00000111653 inhibitor of growth family, member 4 [Source:HGNC Symbol;Acc:19423] NYNRIN ‐0.792954295 ENSG00000205978 NYN domain and retroviral integrase containing [Source:HGNC Symbol;Acc:20165] EPM2AIP1 ‐0.792675375 ENSG00000178567 EPM2A (laforin) interacting protein 1 [Source:HGNC Symbol;Acc:19735] FEZ1 ‐0.791491921 ENSG00000149557 fasciculation and elongation protein zeta 1 (zygin I) [Source:HGNC Symbol;Acc:3659] MYLIP ‐0.78995195 ENSG00000007944 myosin regulatory light chain interacting protein [Source:HGNC Symbol;Acc:21155] HNRNPH2 ‐0.787443972 ENSG00000126945 heterogeneous nuclear ribonucleoprotein H2 (H') [Source:HGNC Symbol;Acc:5042] ZMIZ1 ‐0.785981622 ENSG00000108175 zinc finger, MIZ‐type containing 1 [Source:HGNC Symbol;Acc:16493] CREM ‐0.782638171 ENSG00000095794 cAMP responsive element modulator [Source:HGNC Symbol;Acc:2352] PSPC1 ‐0.781462833 ENSG00000121390 paraspeckle component 1 [Source:HGNC Symbol;Acc:20320] SLC1A1 ‐0.780514323 ENSG00000106688 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 [Source:HGNC Symbol;Acc:109 DOK4 ‐0.780247432 ENSG00000125170 docking protein 4 [Source:HGNC Symbol;Acc:19868] FUBP1 ‐0.776022097 ENSG00000162613 far upstream element (FUSE) binding protein 1 [Source:HGNC Symbol;Acc:4004] FAM59A ‐0.773136178 ENSG00000141441 family with sequence similarity 59, member A [Source:HGNC Symbol;Acc:26136] MPHOSPH8 ‐0.771078283 ENSG00000196199 M‐phase phosphoprotein 8 [Source:HGNC Symbol;Acc:29810] DYNC2LI1 ‐0.770293294 ENSG00000138036 dynein, cytoplasmic 2, light intermediate chain 1 [Source:HGNC Symbol;Acc:24595] DPYSL2 ‐0.768131472 ENSG00000092964 dihydropyrimidinase‐like 2 [Source:HGNC Symbol;Acc:3014] PTPN4 ‐0.767365892 ENSG00000088179 protein tyrosine phosphatase, non‐receptor type 4 (megakaryocyte) [Source:HGNC Symbol;Acc:9656] C14orf147 ‐0.761721205 ENSG00000165389 chromosome 14 open reading frame 147 [Source:HGNC Symbol;Acc:20361] ANK2 ‐0.759315726 ENSG00000145362 ankyrin 2, neuronal [Source:HGNC Symbol;Acc:493] ST3GAL6 ‐0.757613915 ENSG00000064225 ST3 beta‐galactoside alpha‐2,3‐sialyltransferase 6 [Source:HGNC Symbol;Acc:18080] MAP4K3 ‐0.757299936 ENSG00000011566 mitogen‐activated protein kinase kinase kinase kinase 3 [Source:HGNC Symbol;Acc:6865] ARHGEF6 ‐0.755956494 ENSG00000129675 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 [Source:HGNC Symbol;Acc:685] HSD17B4 ‐0.755323753 ENSG00000133835 hydroxysteroid (17‐beta) dehydrogenase 4 [Source:HGNC Symbol;Acc:5213] INSIG1 ‐0.755128375 ENSG00000186480 insulin induced gene 1 [Source:HGNC Symbol;Acc:6083] KIAA0430 ‐0.754422669 ENSG00000166783 KIAA0430 [Source:HGNC Symbol;Acc:29562] C11orf67 ‐0.7534979 ENSG00000087884 chromosome 11 open reading frame 67 [Source:HGNC Symbol;Acc:30205]

86 SCP2 ‐0.750693762 ENSG00000116171 sterol carrier protein 2 [Source:HGNC Symbol;Acc:10606] TUBA1A ‐0.747688611 ENSG00000167552 tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766] GNPAT ‐0.746279123 ENSG00000116906 glyceronephosphate O‐acyltransferase [Source:HGNC Symbol;Acc:4416] USP11 ‐0.744365935 ENSG00000102226 ubiquitin specific peptidase 11 [Source:HGNC Symbol;Acc:12609] VPS45 ‐0.738884833 ENSG00000136631 vacuolar protein sorting 45 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14579] SYN1 ‐0.736029868 ENSG00000008056 synapsin I [Source:HGNC Symbol;Acc:11494] REV1 ‐0.734793143 ENSG00000135945 REV1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14060] PDZD2 ‐0.73347608 ENSG00000133401 PDZ domain containing 2 [Source:HGNC Symbol;Acc:18486] SHOX2 ‐0.731224958 ENSG00000168779 short stature homeobox 2 [Source:HGNC Symbol;Acc:10854] NME4 ‐0.722445279 ENSG00000103202 non‐metastatic cells 4, protein expressed in [Source:HGNC Symbol;Acc:7852] SEP9. ‐0.720147139 ENSG00000184702 septin 5 [Source:HGNC Symbol;Acc:9164] ZMYND8 ‐0.716307376 ENSG00000101040 zinc finger, MYND‐type containing 8 [Source:HGNC Symbol;Acc:9397] GAB2 ‐0.7136122 ENSG00000033327 GRB2‐associated binding protein 2 [Source:HGNC Symbol;Acc:14458] P2RX5 ‐0.713333437 ENSG00000083454 purinergic receptor P2X, ligand‐gated ion channel, 5 [Source:HGNC Symbol;Acc:8536] PTPRA ‐0.710022044 ENSG00000132670 protein tyrosine phosphatase, receptor type, A [Source:HGNC Symbol;Acc:9664] SPRY2 ‐0.708462014 ENSG00000136158 sprouty homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:11270] HMGCR ‐0.704230527 ENSG00000113161 3‐hydroxy‐3‐methylglutaryl‐CoA reductase [Source:HGNC Symbol;Acc:5006] GDPD2 ‐0.702956684 ENSG00000130055 glycerophosphodiester phosphodiesterase domain containing 2 [Source:HGNC Symbol;Acc:25974] GALNT11 ‐0.700703552 ENSG00000178234 UDP‐N‐acetyl‐alpha‐D‐galactosamine:polypeptide N‐acetylgalactosaminyltransferase 11 (GalNAc‐T11) [Source:HGNC Symbol;Acc:198 SETD5 ‐0.700041609 ENSG00000168137 SET domain containing 5 [Source:HGNC Symbol;Acc:25566] RGS19 ‐0.698168495 ENSG00000171700 regulator of G‐protein signaling 19 [Source:HGNC Symbol;Acc:13735] GALNT12 ‐0.698093585 ENSG00000119514 UDP‐N‐acetyl‐alpha‐D‐galactosamine:polypeptide N‐acetylgalactosaminyltransferase 12 (GalNAc‐T12) [Source:HGNC Symbol;Acc:198 GPATCH1 ‐0.697895476 ENSG00000076650 G patch domain containing 1 [Source:HGNC Symbol;Acc:24658] TRIO ‐0.697732804 ENSG00000038382 triple functional domain (PTPRF interacting) [Source:HGNC Symbol;Acc:12303] SLTM ‐0.697127111 ENSG00000137776 SAFB‐like, transcription modulator [Source:HGNC Symbol;Acc:20709] ALDH9A1 ‐0.696270908 ENSG00000143149 aldehyde dehydrogenase 9 family, member A1 [Source:HGNC Symbol;Acc:412] CTDSP2 ‐0.694331407 ENSG00000175215 CTD (carboxy‐terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:HGNC Symbol;Acc:17077] SLC2A10 ‐0.693000691 ENSG00000197496 solute carrier family 2 (facilitated glucose transporter), member 10 [Source:HGNC Symbol;Acc:13444] RAPGEF4 ‐0.690912513 ENSG00000091428 Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:16626] CDHR1 ‐0.689760317 ENSG00000148600 cadherin‐related family member 1 [Source:HGNC Symbol;Acc:14550] SMARCD3 ‐0.687854415 ENSG00000082014 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Source:HGNC Symbol;Acc:11108 GLCE ‐0.686570229 ENSG00000138604 glucuronic acid epimerase [Source:HGNC Symbol;Acc:17855] LILRB1 ‐0.683813191 ENSG00000104972 leukocyte immunoglobulin‐like receptor, subfamily B (with TM and ITIM domains), member 1 [Source:HGNC Symbol;Acc:6605] ATP10A ‐0.683263405 ENSG00000206190 ATPase, class V, type 10A [Source:HGNC Symbol;Acc:13542] NPTX2 ‐0.681753243 ENSG00000106236 neuronal pentraxin II [Source:HGNC Symbol;Acc:7953]

87 STK19 ‐0.680702725 ENSG00000204344 serine/threonine kinase 19 [Source:HGNC Symbol;Acc:11398] PAPSS1 ‐0.679673084 ENSG00000138801 3'‐phosphoadenosine 5'‐phosphosulfate synthase 1 [Source:HGNC Symbol;Acc:8603] MPP2 ‐0.677929489 ENSG00000108852 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2) [Source:HGNC Symbol;Acc:7220] DUSP26 ‐0.677167074 ENSG00000133878 dual specificity phosphatase 26 (putative) [Source:HGNC Symbol;Acc:28161] C12orf35 ‐0.676954586 ENSG00000174718 chromosome 12 open reading frame 35 [Source:HGNC Symbol;Acc:25559] HMG20A ‐0.674529225 ENSG00000140382 high‐mobility group 20A [Source:HGNC Symbol;Acc:5001] ARHGEF40 ‐0.673551027 ENSG00000165801 Rho guanine nucleotide exchange factor (GEF) 40 [Source:HGNC Symbol;Acc:25516] C15orf39 ‐0.668481408 ENSG00000167173 chromosome 15 open reading frame 39 [Source:HGNC Symbol;Acc:24497] VWA1 ‐0.667115804 ENSG00000179403 von Willebrand factor A domain containing 1 [Source:HGNC Symbol;Acc:30910] KDM3B ‐0.664444785 ENSG00000120733 lysine (K)‐specific demethylase 3B [Source:HGNC Symbol;Acc:1337] DENND1A ‐0.661715594 ENSG00000119522 DENN/MADD domain containing 1A [Source:HGNC Symbol;Acc:29324] CRB1 ‐0.659630965 ENSG00000134376 crumbs homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:2343] ALKBH4 ‐0.657779637 ENSG00000160993 alkB, alkylation repair homolog 4 (E. coli) [Source:HGNC Symbol;Acc:21900] KDM3A ‐0.654551818 ENSG00000115548 lysine (K)‐specific demethylase 3A [Source:HGNC Symbol;Acc:20815] FIP1L1 ‐0.652884005 ENSG00000145216 FIP1 like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:19124] JUP ‐0.651985401 ENSG00000173801 junction plakoglobin [Source:HGNC Symbol;Acc:6207] ODZ4 ‐0.650783807 ENSG00000149256 odz, odd Oz/ten‐m homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:29945] FGGY ‐0.650567353 ENSG00000172456 FGGY carbohydrate kinase domain containing [Source:HGNC Symbol;Acc:25610] SSB ‐0.650499083 ENSG00000138385 Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316] PMS2P1 ‐0.649371142 ENSG00000078319 postmeiotic segregation increased 2 pseudogene 1 [Source:HGNC Symbol;Acc:9123] CUX1 ‐0.646832383 ENSG00000160967 cut‐like homeobox 1 [Source:HGNC Symbol;Acc:2557] BPTF ‐0.64661751 ENSG00000171634 bromodomain PHD finger transcription factor [Source:HGNC Symbol;Acc:3581] NDRG2 ‐0.645733052 ENSG00000165795 NDRG family member 2 [Source:HGNC Symbol;Acc:14460] WDR91 ‐0.644325821 ENSG00000105875 WD repeat domain 91 [Source:HGNC Symbol;Acc:24997] NCBP2 ‐0.642540522 ENSG00000114503 nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659] MTMR9 ‐0.642277929 ENSG00000104643 myotubularin related protein 9 [Source:HGNC Symbol;Acc:14596] ASAP3 ‐0.640110039 ENSG00000088280 ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 [Source:HGNC Symbol;Acc:14987] LPAR4 ‐0.638012977 ENSG00000147145 lysophosphatidic acid receptor 4 [Source:HGNC Symbol;Acc:4478] PIGH ‐0.631913671 ENSG00000100564 phosphatidylinositol glycan anchor biosynthesis, class H [Source:HGNC Symbol;Acc:8964] RNF130 ‐0.629938586 ENSG00000113269 ring finger protein 130 [Source:HGNC Symbol;Acc:18280] CDH15 ‐0.627242735 ENSG00000129910 cadherin 15, type 1, M‐cadherin (myotubule) [Source:HGNC Symbol;Acc:1754] ACSL3 ‐0.624988796 ENSG00000123983 acyl‐CoA synthetase long‐chain family member 3 [Source:HGNC Symbol;Acc:3570] STRADA ‐0.624794267 ENSG00000125695 STE20‐related kinase adaptor alpha [Source:HGNC Symbol;Acc:30172] KRCC1 ‐0.623963265 ENSG00000172086 lysine‐rich coiled‐coil 1 [Source:HGNC Symbol;Acc:28039] FCHSD2 ‐0.623017347 ENSG00000137478 FCH and double SH3 domains 2 [Source:HGNC Symbol;Acc:29114]

88 CHMP7 ‐0.621463765 ENSG00000147457 CHMP family, member 7 [Source:HGNC Symbol;Acc:28439] S100PBP ‐0.619414606 ENSG00000116497 S100P binding protein [Source:HGNC Symbol;Acc:25768] PAXIP1 ‐0.618535695 ENSG00000157212 PAX interacting (with transcription‐activation domain) protein 1 [Source:HGNC Symbol;Acc:8624] CHMP2A ‐0.618504496 ENSG00000130724 chromatin modifying protein 2A [Source:HGNC Symbol;Acc:30216] OFD1 ‐0.616485015 ENSG00000046651 oral‐facial‐digital syndrome 1 [Source:HGNC Symbol;Acc:2567] PPA2 ‐0.614897466 ENSG00000138777 pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883] PUF60 ‐0.614693561 ENSG00000179950 poly‐U binding splicing factor 60KDa [Source:HGNC Symbol;Acc:17042] PNMA1 ‐0.609766571 ENSG00000176903 paraneoplastic antigen MA1 [Source:HGNC Symbol;Acc:9158] C3orf63 ‐0.60655848 ENSG00000163946 chromosome 3 open reading frame 63 [Source:HGNC Symbol;Acc:30314] MOAP1 ‐0.606538839 ENSG00000165943 modulator of apoptosis 1 [Source:HGNC Symbol;Acc:16658] ID3 ‐0.606408536 ENSG00000117318 inhibitor of DNA binding 3, dominant negative helix‐loop‐helix protein [Source:HGNC Symbol;Acc:5362] CACNB3 ‐0.605159604 ENSG00000167535 calcium channel, voltage‐dependent, beta 3 subunit [Source:HGNC Symbol;Acc:1403] PNPLA3 ‐0.604297354 ENSG00000100344 patatin‐like phospholipase domain containing 3 [Source:HGNC Symbol;Acc:18590] C1orf123 ‐0.601970883 ENSG00000162384 chromosome 1 open reading frame 123 [Source:HGNC Symbol;Acc:26059] C2orf72 ‐0.600018567 ENSG00000204128 chromosome 2 open reading frame 72 [Source:HGNC Symbol;Acc:27418]

89 Supplementary Table S4: Table showing ARACNE‐identified TFs in the TCGA MES tumor network classifed as G‐CIMP based on data obtained from Noushmehr et al., 2010. The venn diagram on the right shows the overlap of the G‐CIMP genes (i.e. hypermethylated in the PN group) and ARACNE‐identified TAZ target genes. 12% of the TAZ‐target genes are in the G‐CIMP group.

Hub a/r CIMP gene? CEBPB activator No ELF4 activator Yes MAFB activator No HCLS1 activator Yes FOSL2 activator No WWTR1 activator Yes ZNF217 activator Yes LASS2 activator No TRIM22 activator No YAP1 activator No STAT3 activator No LZTS1 activator No MYT1L repressor No THRA repressor No ZNF238 repressor No ASCL1 repressor No

90 Supp Table S5: List of primers used for ChIP analyses

Gene Primer sequence ACTG2 F TGTTTATCGACTGGCTGTGC ACTG2 R AAGCTCCCCCTCTGATTCTC ACTN F TTCTAGTCCAGCCACGTTGA ACTN R ATTTGCTGAGCACCATCTGC ADAMTS1 F TTGAGTGAAAGCACGCAGAC ADAMTS1 R GCCACCTCTTCACCAGAGAC ANGPTL4 F TCCCCTTCCTGACAGGGTAT ANGPTL4 R GAGCCTGGGGTAGGGATAGA CD44 F AAGACTGCCTGGTGTTCTCC CD44 R AGAAATGCACCCAGCCATC COL1A1 F ATTAACGAACAAAAAGGAGTCAA COL1A1 R GATCCTGGATGAGGGGGTA CTGF F TTCTGTGAGCTGGAGTGTGC CTGF R GCCAATGAGCTGAATGGAGT CXCL2 F TCAGCTAAACAGGCTTGGAAA CXCL2 R AAGGCCATAGACACCACCAG E2F7 F AGTGAATGGTGGGAACAAAG E2F7 R AGTCTTCGGGGCCATCCT IL4R F ACTATCCAAATGTGGCTGGAG IL4R R TCCTCCTCCCCTTCCTAACA IQGAP F CTCACCTCTCTGCCCTTCAC IQGAP R CAGTCTCTTCCTGGGTCTGTG LUM F GAAGCAGGACTCAATTCTTGG LUM R ATCTTGTGGTGTGGCATGTG MYH9 F AATACGTCTGCCCATCAAGG MYH9 R GTCAGCCTTGCTTAGCCTTC TAGLN F TACTAGGGCTCGGCTACCAG TAGLN R GACTCACCTAGGGGGTCAGC TIMP1 F TGACCCACTCACTTGCTTCTT TIMP1 R CTGGCACCAGGGTTGTAACT TUBB F GCTAGAATTAAAATCCAAGTCACC TUBB R CTCTTCGTCCTGGTGTTTCC

91