Supplementary Table 4. The list of genes differentially expressed in CDK12 inactivated tumors (raw p-values are shown) GeneID Validated_Inhouse Validated_TCGA_RNAseq FoldChange_TCGA_Affy_NormalizedFoldChange_Affy_InHouse_Rawlog10PValue_TCGA_Affy_Normalizedlog10PValue_TCGA_RNAseq_Normalizedlog10PValue_Affy_InHouse_RawMean_TCGA_Affy SD_TCGA_Affy Mean_TCGA_RNAseq SD_TCGA_RNAseq Confounding_CN log10PValue_TCGA_RNAseq_CNENTREZ DESCRIPTION RPRD1A FC&PV FC&PV -2.8 -2.8 7 6.4 1.3 6.6 1.4 3.9 0.9 55197 regulation of nuclear pre-mRNA domain containing 1A BCCIP FC&PV FC -2.2 -1.8 8.1 0 1.5 5.7 0.8 4.1 0.4 56647 BRCA2 and CDKN1A interacting protein TERF2 FC FC&PV -1.9 -1.5 5.9 0 1 6.3 0.8 3.3 0.5 7014 telomeric repeat binding factor 2 SF3A3 Not_FC FC&PV 1.6 -0.8 3.5 0 0.8 6.9 0.6 5.2 0.5 CN 1.3 10946 splicing factor 3a, subunit 3, 60kDa THADA FC&PV FC -1.6 -1.1 3.4 0 2.8 6.2 0.7 2.2 0.4 63892 thyroid adenoma associated DENND1A Not_FC FC 1.5 -0.4 4.6 0.3 0.6 5.5 1.1 2.9 0.5 57706 DENN/MADD domain containing 1A CSTF3 Not_FC FC -1.4 0.5 4.8 0 0.6 6.8 0.6 3.7 0.5 CN_FC_oposite1.5 1479 cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa NRAS FC&PV FC&PV 1.4 1 8.1 1.5 1.6 6.8 1 4.5 0.6 4893 neuroblastoma RAS viral (v-ras) oncogene homolog WDR5B FC&PV FC&PV -1.4 -1.9 4.4 0 2.6 5.9 0.8 2.6 0.5 54554 WD repeat domain 5B BBS1 FC FC&PV -1.3 -0.8 3.8 0 1 7 0.6 4 0.5 582 Bardet-Biedl syndrome 1 ORMDL2 FC FC&PV -1.3 -1.6 3.5 3.7 0.7 8 0.6 4.9 0.7 29095 ORMDL sphingolipid biosynthesis regulator 2 TMEM5 FC&PV FC&PV -1.3 -1.2 6 0 1.9 7.9 0.7 3.1 0.5 CN -1.4 10329 transmembrane protein 5 CIRBP Not_FC FC -1.2 0.7 3.8 1 1 7.5 0.8 4.7 0.6 1153 cold inducible RNA binding protein MRPS7 FC FC&PV -1.2 -0.9 4.1 2.7 0.9 7 0.8 4.6 0.6 CN -1.8 51081 mitochondrial ribosomal protein S7 MTX2 FC FC&PV 1.2 0.4 3.5 1.7 0.8 8.3 0.6 5 0.5 10651 metaxin 2 PPP3CB FC FC&PV -1.2 -1.2 3.1 0 0.7 6.7 0.5 3.4 0.5 5532 protein phosphatase 3, catalytic subunit, beta isozyme SHQ1 FC FC -1.2 -0.5 3.6 0 0.6 7 0.5 3.2 0.4 55164 SHQ1, H/ACA ribonucleoprotein assembly factor DNAJB4 FC FC 1.2 0.8 3.3 0.5 0.7 5.1 0.6 2.8 0.6 11080 DnaJ (Hsp40) homolog, subfamily B, member 4 TNFSF10 FC&PV FC&PV 1.2 2.6 5.6 4.6 1.9 9 1.7 5.8 1.7 CN 2.5 8743 tumor necrosis factor (ligand) superfamily, member 10 GLUL FC&PV FC 1.2 1.1 4.4 0.9 7.1 8.2 0.6 6.7 0.6 2752 glutamate-ammonia ligase C1orf109 Not_FC&PV FC&PV 1.1 -0.6 3.1 1.4 1.6 6.2 0.7 3.5 0.6 CN 1.3 54955 chromosome 1 open reading frame 109 SURF1 Not FC&PV -1.1 3.9 2.8 8.3 0.6 4.5 0.6 6834 surfeit 1 H2AFY2 Not FC&PV -1.1 3.3 1.8 5.7 0.7 4.1 1 55506 H2A histone family, member Y2 SNF8 FC FC&PV -1.1 -0.5 3.8 3.4 0.4 6.9 0.7 5 0.6 CN -1.5 11267 SNF8, ESCRT-II complex subunit NKIRAS2 FC FC&PV -1.1 -0.9 3.1 3.3 0.7 5.1 0.5 4.4 0.5 CN -2 28511 NFKB inhibitor interacting Ras-like 2 TSC1 FC FC -1.1 -0.5 6.1 0 0.6 5.4 0.5 2 0.5 7248 tuberous sclerosis 1 CSNK2A2 FC FC -1.1 -1.3 3.2 0 0.7 6.2 0.7 3.9 0.5 1459 casein kinase 2, alpha prime polypeptide KRCC1 FC&PV FC&PV 1.1 0.9 4 2.5 1.5 8.3 0.8 4.7 0.7 CN_FC_oposite-1.7 51315 lysine-rich coiled-coil 1 CD59 FC&PV FC&PV 1.1 1.6 3.2 2.6 8.7 8.6 0.8 5.3 0.8 CN 1.6 966 CD59 molecule, complement regulatory protein DOLK Not FC&PV -1 3.3 2.3 5.2 0.5 3.4 0.5 22845 dolichol kinase ABHD11 Not FC&PV -1 3.1 3.2 7.9 0.7 5.8 0.9 83451 abhydrolase domain containing 11 PDE9A FC FC&PV -1 -0.7 4.5 2.3 0.5 4.8 1 2.5 1.1 5152 phosphodiesterase 9A AGK FC FC&PV -1 -0.4 3.8 0 0.5 6.4 0.5 3.4 0.4 55750 acylglycerol kinase ERLIN2 FC FC -1 -1.5 3.8 1.2 1.2 5.7 1 3.1 0.7 11160 ER lipid raft associated 2 NQO2 FC FC 1 1.2 3.5 1.3 0.9 6.5 0.9 3 0.7 4835 NAD (P)H dehydrogenase, quinone 2 PIGP FC&PV FC&PV -1 -1.1 3.8 4.7 2.5 8.3 0.7 4 0.6 51227 phosphatidylinositol glycan anchor biosynthesis, class P UGGT2 Not_FC&PV Not -1.5 -1.9 7.7 0 3.1 4.9 0.7 1.6 0.4 55757 UDP-glucose glycoprotein glucosyltransferase 2 ALG13 Not_FC&PV Not -1.2 -1 5.3 0 2.2 4.8 0.8 2.6 0.5 79868 ALG13, UDP-N-acetylglucosaminyltransferase subunit INTS6 Not_FC&PV Not -1 -1.4 3.2 0 5.9 6 0.6 2.1 0.5 26512 integrator complex subunit 6 ERCC8 NA Not -1.1 4.9 0 4.8 0.5 1.2 0.3 1161 excision repair cross-complementation group 8 GRB2 FC&PV FC -0.9 -0.5 3.5 0 1.9 7.2 0.5 5.3 0.4 CN -1.6 2885 growth factor receptor-bound protein 2 IFT88 FC&PV FC -0.8 -1.3 2.9 0 2.4 5.4 0.5 1.3 0.3 8100 intraflagellar transport 88 FADS1 FC&PV FC -0.8 -1.7 2.7 0.3 7.8 5.4 1.1 2.7 1.2 3992 fatty acid desaturase 1 PIBF1 FC&PV FC -0.8 -2.3 2.5 0 4 5.4 0.7 1.9 0.5 10464 progesterone immunomodulatory binding factor 1 PCYT2 FC&PV FC -0.7 -1.1 2.4 1.2 3.5 5.1 0.6 4.3 0.7 CN -1.3 5833 phosphate cytidylyltransferase 2, ethanolamine TM9SF4 FC&PV FC 0.8 0.9 2.2 0 3.5 6.3 0.6 5.5 0.5 9777 transmembrane 9 superfamily protein member 4 IMPDH2 FC&PV FC -0.7 -0.8 2.2 1.1 1.7 9.7 0.7 6.4 0.8 3615 IMP (inosine 5'-monophosphate) dehydrogenase 2 HN1L FC&PV FC 0.8 1.1 2.1 0.6 1.4 6.2 0.6 5.3 0.6 90861 hematological and neurological expressed 1-like CDKN2A FC&PV FC&PV 0.7 1.3 4.4 2.5 2.1 6.6 1 6.6 1.7 1029 cyclin-dependent kinase inhibitor 2A TMEM223 FC&PV FC&PV -0.9 -1 3.4 1.9 1.6 8.3 0.5 5.1 0.5 79064 transmembrane protein 223 C11orf71 FC&PV FC&PV -0.9 -0.4 3.4 4.5 2.3 5.6 0.9 3 0.7 54494 chromosome 11 open reading frame 71 FOXK2 FC&PV FC&PV -0.8 -1.9 3 1.9 6 6 0.6 4.1 0.5 CN -2.9 3607 forkhead box K2 EPM2AIP1 FC&PV FC&PV -1.4 -0.8 3 3 4.8 7.3 0.6 3 0.6 9852 EPM2A (laforin) interacting protein 1 YTHDF1 FC&PV FC&PV -0.8 -0.7 2.9 0 1.4 8.2 0.6 4.5 0.5 CN -2 54915 YTH N (6)-methyladenosine RNA binding protein 1 NOTCH2 FC&PV FC&PV 1.1 0.5 2.9 1.9 2.5 6.8 0.6 4.4 0.7 4853 notch 2 TAGLN2 FC&PV FC&PV 0.9 0.6 2.9 1.4 2.9 8.4 0.5 8.4 0.6 8407 transgelin 2 MRPL12 FC&PV FC&PV -0.6 -0.9 2.7 2.3 1.4 7 0.6 6.5 0.8 CN -1.8 6182 mitochondrial ribosomal protein L12 TTI1 FC&PV FC&PV -0.8 -1.4 2.7 3 6.2 6.3 0.7 3.7 0.6 CN -4.2 9675 TELO2 interacting protein 1 FADS3 FC&PV FC&PV 1 1.2 2.7 1.5 6.3 5.2 0.5 4.7 0.6 3995 fatty acid desaturase 3 HEBP2 FC&PV FC&PV 1 1.3 2.6 1.6 3.3 9.7 0.7 6.1 0.8 23593 heme binding protein 2 ZNF512B FC&PV FC&PV -0.7 -0.5 2.6 2.9 1.4 5.9 0.6 3.6 0.6 CN -1.9 57473 zinc finger protein 512B ZNF195 FC&PV FC&PV 1.2 1.2 2.5 3.6 1.4 6.3 0.9 3.2 0.7 CN 2.9 7748 zinc finger protein 195 CFI FC&PV FC&PV 0.9 1.5 2.5 2.4 1.4 8.3 1.1 5.1 1.1 3426 complement factor I GCLM FC&PV FC&PV 0.9 1.3 2.5 2.1 1.3 6.7 0.8 3 0.6 2730 glutamate-cysteine ligase, modifier subunit SEZ6L2 FC&PV FC&PV 0.6 1.4 2.5 2.4 1.6 5.8 0.9 4.6 0.9 26470 seizure related 6 homolog (mouse)-like 2 TMEM41B FC&PV FC&PV 0.7 0.7 2.4 0 1.5 6.8 0.7 3 0.5 CN 2.3 440026 transmembrane protein 41B SPP1 FC&PV FC&PV 0.8 1.8 2.4 1.5 10.4 10.3 1.2 7.5 1.4 6696 secreted phosphoprotein 1 IFNGR1 FC&PV FC&PV 0.6 1.2 2.4 1.9 1.5 7.5 0.7 5 0.6 3459 interferon gamma receptor 1 PARVA FC&PV FC&PV 0.6 0.4 2.3 5.6 1.4 6.6 0.6 3.5 0.5 CN 2.4 55742 parvin, alpha GINS1 FC&PV FC&PV -0.7 -1.4 2.3 1.3 4.5 8 0.7 3 0.6 9837 GINS complex subunit 1 (Psf1 homolog) RBM8A FC&PV FC&PV -0.9 -1.6 2.3 0 3.4 7.1 0.8 4.6 0.6 9939 RNA binding motif protein 8A SWAP70 FC&PV FC&PV 1.1 0.9 2.2 0 1.3 5.5 0.7 2.6 0.6 CN 2.1 23075 SWAP switching B-cell complex 70kDa subunit HGSNAT FC&PV FC&PV 0.7 0.5 2.1 1.9 1.3 7 0.8 4.5 0.7 138050 heparan-alpha-glucosaminide N-acetyltransferase CTSD FC&PV FC&PV 0.9 1.5 2.1 1.7 9.2 6.2 0.7 8.8 0.8 CN 2.3 1509 cathepsin D TMEM50A FC&PV FC&PV 0.7 0.6 2.1 1.8 2.5 8.1 0.7 6.2 0.5 CN 1.7 23585 transmembrane protein 50A CA12 FC&PV FC&PV 1 3.6 2.1 1.9 2.7 5.4 1.4 3.1 1.6 771 carbonic anhydrase XII PPP1CB FC&PV FC&PV 0.9 1.4 2.1 1.3 1.9 8.2 0.5 6.2 0.6 5500 protein phosphatase 1, catalytic subunit, beta isozyme SGMS1 FC&PV FC&PV 0.8 0.7 2.1 1.5 1.3 6.4 0.9 3.2 0.7 259230 sphingomyelin synthase 1 PSMA1 FC&PV FC&PV 0.7 0.8 2.1 0 6.4 10 0.6 5.5 0.5 1.3 5682 proteasome subunit alpha 1 DCP1B FC&PV RNAseq_only -2 5.7 2 3.6 0.6 196513 decapping mRNA 1B HACL1 FC&PV RNAseq_only 1.1 4.8 1.4 3.2 0.5 26061 2-hydroxyacyl-CoA lyase 1 CPNE2 FC&PV RNAseq_only 1.8 4 1.7 4.3 0.8 221184 copine II OSMR FC&PV RNAseq_only 2.6 3.7 2.8 3.1 1.1 9180 oncostatin M receptor ATL3 FC&PV RNAseq_only 2.5 3.6 1.9 3.8 0.7 25923 atlastin GTPase 3 TMEM189 FC&PV RNAseq_only -0.4 3.4 2.8 4.5 0.6 CN -2.5 387521 transmembrane protein 189 OXLD1 FC&PV RNAseq_only -1 3.3 4.6 4.3 0.7 CN -1.8 339229 oxidoreductase-like domain containing 1 TCTEX1D2 FC&PV RNAseq_only 1.3 3.3 1.4 4 1 255758 Tctex1 domain containing 2 FAM114A1 FC&PV RNAseq_only 2 3.1 2 3.4 0.8 92689 family with sequence similarity 114, member A1 VPS25 FC&PV RNAseq_only -0.7 3.1 1.4 5.7 0.6 CN -2.1 84313 vacuolar protein sorting 25 homolog (S.