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Home , Acylglycerol kinase, AK2, BCKDHA, DCP1B, Dolichol kinase, RecQ helicase

Supplementary Table 4. The list of 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 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 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 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 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 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 , 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 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 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 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 -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. cerevisiae) ARL16 FC&PV RNAseq_only -1.3 3 1.4 4.1 0.5 CN -1.8 339231 ADP-ribosylation factor-like 16 FAM160A2 FC&PV RNAseq_only 0.6 2.8 3.8 3.3 0.6 CN 2.3 84067 family with sequence similarity 160, member A2 FAM120AOS FC&PV RNAseq_only -1 2.4 2.1 3.5 0.5 158293 family with sequence similarity 120A opposite strand MFN2 FC&PV RNAseq_only 0.8 2 2.9 4.4 0.5 CN 1.7 9927 mitofusin 2 TRNAU1AP FC FC 0.9 0.5 3.3 1 0.4 5.7 0.6 3 0.5 54952 tRNA selenocysteine 1 associated protein 1 PTPRU FC FC 0.8 0.5 3.2 1 0.2 5.2 0.7 4 1.1 10076 protein tyrosine phosphatase, receptor type, U LZTFL1 FC FC 0.6 0.4 2.8 0.9 1.2 6.3 0.9 3.4 0.5 54585 zipper transcription factor-like 1 FANCI FC FC -0.8 -1.7 2.8 1 1.1 6.1 0.9 3 0.6 55215 , complementation group I ZGPAT FC FC -0.8 -1.2 2.6 0.3 1.2 5.7 0.6 4 0.7 CN -1.9 84619 zinc finger, CCCH-type with G patch domain KLF7 FC FC 1 0.5 2.5 0 0.3 5.6 0.9 2.2 0.8 8609 Kruppel-like factor 7 (ubiquitous) ZMYM2 FC FC -0.6 -0.7 2.5 0.9 1.3 5.5 0.5 2.7 0.5 7750 zinc finger, MYM-type 2 THAP10 FC FC 0.8 1.1 2.5 0 0.6 5.8 0.8 2.5 0.5 56906 THAP domain containing 10 ALG9 FC FC 0.7 0.9 2.4 0 1 5.9 0.7 2.2 0.4 79796 ALG9, alpha-1,2-mannosyltransferase COQ2 FC FC 0.6 1.2 2.3 0 1 6.1 0.7 2.6 0.5 27235 coenzyme Q2 4-hydroxybenzoate polyprenyltransferase MRPS16 FC FC -0.6 -0.4 2.3 0 0.4 7.7 0.6 5.1 0.4 51021 mitochondrial ribosomal protein S16 KLHL21 FC FC 0.6 0.7 2.2 1.1 0.7 6.7 0.7 2.9 0.7 9903 kelch-like family member 21 ENAH FC FC -0.8 -1.5 2.1 1.1 0.7 7.6 0.6 3.2 0.6 55740 enabled homolog (Drosophila) C5orf28 FC FC 0.8 0.8 2.1 0.7 0.9 6.2 0.6 3.1 0.5 64417 chromosome 5 open reading frame 28 CLN3 FC FC 0.6 1.3 2.1 0.8 1 5.7 0.5 4.5 0.5 1201 ceroid-lipofuscinosis, neuronal 3 SRPX FC FC -0.5 -1.1 2.1 0 0.7 4.7 0.9 1.6 0.7 8406 sushi-repeat containing protein, X-linked RPL31 FC FC -0.7 -1 2.1 1 1 8.9 0.5 7.3 0.7 6160 ribosomal protein L31 ADNP FC FC -0.6 -0.8 2 0.7 1.1 8.6 0.6 4.9 0.5 CN -2.6 23394 activity-dependent neuroprotector homeobox TM7SF2 FC FC&PV -0.9 -1 3.8 3 0.5 6 0.8 4.8 0.9 7108 transmembrane 7 superfamily member 2 SGSM2 FC FC&PV -0.7 -1 3.4 3.2 1 5.6 0.5 2.5 0.6 CN -3.3 9905 small G protein signaling modulator 2 MT1X FC FC&PV 0.9 1.4 3.3 1.6 1.2 8 1.1 5.8 1.1 4501 metallothionein 1X NEK11 FC FC&PV -0.8 -0.4 3.2 0 0.4 5.2 0.8 2.1 0.6 CN -1.4 79858 NIMA-related kinase 11 NYNRIN FC FC&PV 0.8 0.5 3.2 2 0.5 6.2 0.8 4.2 0.9 CN_FC_oposite-1.7 57523 NYN domain and retroviral containing OSBPL3 FC FC&PV 0.8 1.8 3.2 3.2 0.5 5.6 0.9 3 0.9 26031 oxysterol binding protein-like 3 PRPSAP1 FC FC&PV -0.8 -0.9 3.1 2.1 0.8 7.3 0.6 4 0.5 CN -2 5635 phosphoribosyl pyrophosphate synthetase-associated protein 1 PTEN FC FC&PV 1.2 0.8 3 1.4 0.6 5.6 0.9 3.8 0.7 CN 1.8 5728 phosphatase and tensin homolog REC8 FC FC&PV -0.9 -1.1 2.9 1.4 1.1 6.9 1.1 5.5 1.3 CN -1.7 9985 REC8 meiotic recombination protein POT1 FC FC&PV -1 -1.2 2.9 2.7 1 6.1 0.6 2.9 0.5 25913 protection of telomeres 1 VAMP3 FC FC&PV 0.8 0.7 2.9 1.8 0.8 7.7 0.9 5.6 0.5 9341 vesicle-associated membrane protein 3 NSF FC FC&PV -0.8 -0.9 2.8 1.9 0.5 6.8 0.7 3.3 0.6 CN -1.6 4905 N-ethylmaleimide-sensitive factor CCND1 FC FC&PV -0.5 -1.3 2.8 2.1 0.9 5.5 1.4 4.5 1.6 595 cyclin D1 CAT FC FC&PV 1 0.8 2.7 1.9 0.5 8.2 0.8 5.4 0.8 CN 1.7 847 catalase ISCA1 FC FC&PV 0.8 0.6 2.6 2.3 0.3 6.9 0.7 4.2 0.6 CN 1.5 81689 iron-sulfur cluster assembly 1 ORC3 FC FC&PV -1 -1.3 2.6 1.7 1.2 6.5 0.8 3.5 0.7 23595 origin recognition complex, subunit 3 CANT1 FC FC&PV -0.9 -0.4 2.5 1.8 0.2 6.7 0.6 4.7 0.5 CN -1.8 124583 calcium activated nucleotidase 1 NFYC FC FC&PV 0.9 0.6 2.5 2.8 0.6 5.8 0.5 4.5 0.5 CN 1.7 4802 nuclear transcription factor Y, gamma IRS1 FC FC&PV 0.9 0.5 2.4 0 0.1 5.1 1.1 2 0.9 3667 insulin receptor 1 NTAN1 FC FC&PV 0.9 1.1 2.4 1.9 0.6 5.9 0.8 4.3 0.6 123803 N-terminal asparagine amidase PDHA1 FC FC&PV 0.8 0.9 2.4 2.1 1.1 8.4 0.7 4.6 0.6 5160 lipoamide) alpha 1 ERCC1 FC FC&PV -0.6 -0.4 2.4 2.6 0.3 6.1 0.7 5.1 0.6 2067 excision repair cross-complementation group 1 MXRA7 FC FC&PV -0.9 -0.7 2.3 1.3 0.6 9.1 0.8 4.3 0.9 CN -2.6 439921 matrix-remodelling associated 7 ZC3H7A FC FC&PV 1.3 1.4 2.3 0 0.7 5.9 0.6 3.1 0.6 29066 zinc finger CCCH-type containing 7A LRP8 FC FC&PV 0.9 0.9 2.3 0 0.6 5.5 0.9 2.1 0.8 7804 low density lipoprotein receptor-related 8, apolipoprotein e receptor ADK FC FC&PV 0.7 1.4 2.3 1.3 1.1 6 0.8 3.5 0.7 132 adenosine kinase COPS6 FC FC&PV -0.9 -1 2.3 0 1.2 7.4 0.5 6.1 0.6 10980 COP9 signalosome subunit 6 AMZ2 FC FC&PV -0.8 -0.9 2.2 1.4 1.1 7.9 0.6 4.4 0.5 CN -1.4 51321 archaelysin family metallopeptidase 2 RNASEH2A FC FC&PV -0.7 -1.2 2.2 2 1.3 7.4 0.9 5.2 0.8 10535 ribonuclease H2, subunit A AP3B1 FC FC&PV -0.8 -1.1 2.1 0 0.7 5.1 0.6 3.5 0.6 8546 adaptor-related 3, beta 1 subunit NPLOC4 FC FC&PV -0.7 -0.5 2.1 2 0.8 6.7 0.5 3.9 0.5 CN -1.7 55666 NPL4 homolog, ubiquitin recognition factor BLCAP FC FC&PV -0.7 -0.9 2.1 1.3 1.1 8.7 0.5 5.2 0.5 CN -4 10904 bladder associated protein C17orf62 FC FC&PV -0.8 -0.5 2.1 1.6 0.4 6.9 0.5 4.3 0.5 CN -2.5 79415 open reading frame 62 SPAG4 FC FC&PV -0.6 -0.8 2.1 1.4 1 5.1 1 3 1 6676 sperm associated antigen 4 ZHX2 FC FC&PV -0.9 -0.5 2.1 1.8 0.4 6.8 1.1 3.9 1.1 22882 zinc fingers and homeoboxes 2 SURF2 FC FC&PV -0.7 -0.4 2 2.5 0.9 5.9 0.4 4.2 0.5 6835 surfeit 2 ATP10D FC Not -0.9 0.5 2.9 0 0.3 5 0.9 1.2 0.5 57205 ATPase, class V, type 10D CBX5 FC Not 1 -1 2.6 0.2 0.8 6.6 0.7 4.1 0.7 23468 chromobox homolog 5 DIRC2 FC RNAseq_only 1.5 4.3 0.8 2.9 0.5 84925 disrupted in renal carcinoma 2 TTC30B FC RNAseq_only -1.9 4.1 1 2.6 0.7 150737 tetratricopeptide repeat domain 30B ZNF117 FC RNAseq_only 1.2 4.1 0.5 2.9 1 51351 zinc finger protein 117 MIF4GD FC RNAseq_only -0.8 4 0.5 4.2 0.6 CN -1.8 57409 MIF4G domain containing DNAJC30 FC RNAseq_only -0.7 3.6 0.4 3.8 0.6 84277 DnaJ (Hsp40) homolog, subfamily C, member 30 PLXDC2 FC RNAseq_only 0.9 3.4 0.8 3.9 1 84898 plexin domain containing 2 SH3BP5L FC RNAseq_only -0.5 3.2 0.3 3.4 0.5 CN -1.3 80851 SH3-binding domain protein 5-like MDP1 FC RNAseq_only -0.5 3.1 1.2 2.7 0.6 CN -1.7 145553 magnesium-dependent phosphatase 1 TMEM246 FC RNAseq_only -1.2 3.1 0.5 2.3 1.3 84302 transmembrane protein 246 PRMT6 FC RNAseq_only -1.4 2.9 0.7 3.4 0.7 55170 protein arginine methyltransferase 6 ZNF740 FC RNAseq_only -0.7 2.6 0.6 3.2 0.5 CN -2.5 283337 zinc finger protein 740 C17orf89 FC RNAseq_only -1.6 2.6 1.2 5.1 0.9 CN -1.8 284184 chromosome 17 open reading frame 89 METTL16 FC RNAseq_only -0.6 2.4 1.1 2.5 0.5 CN -3.3 79066 methyltransferase like 16 ATP6V0A1 FC RNAseq_only -0.8 2.3 0.9 3 0.6 CN -2.1 535 ATPase, H+ transporting, lysosomal V0 subunit a1 ACVR1B FC RNAseq_only -0.8 2 1.1 3.8 0.6 CN -1.4 91 activin A receptor, type IB SDC1 Not_FC FC -0.8 0.6 3.1 1.1 1.2 4.9 1 3.5 1.3 6382 syndecan 1 SETX Not_FC FC -0.9 0.7 3 0 0.7 5.6 0.5 2.3 0.4 23064 senataxin AK2 Not_FC FC 1.1 -1.2 2.8 0.8 0.7 6.8 0.7 5.3 0.6 204 2 LRRC6 Not_FC FC -0.8 0.5 2.8 0 0.3 4.9 0.8 2 0.8 23639 leucine rich repeat containing 6 POLR3C Not_FC FC 0.9 -0.5 2.4 0 0.7 5.9 0.7 4.6 0.6 10623 (RNA) III (DNA directed) polypeptide C 62kD TMEM39B Not_FC FC 0.9 -0.8 2.3 0.9 0.6 5.6 0.6 3.9 0.5 CN 1.6 55116 transmembrane protein 39B DNMT3B Not_FC FC -0.7 0.5 2.2 0 0.2 5.2 0.6 1.9 0.7 1789 DNA (cytosine-5-)-methyltransferase 3 beta LGALS3BP Not_FC FC -0.6 0.5 2.1 0.7 0.4 9.1 0.6 9.3 0.7 -1.8 3959 lectin, galactoside-binding, soluble, 3 binding protein YRDC Not_FC FC 0.9 -0.6 2 0.6 0.5 6.6 0.7 4.2 0.6 CN 1.3 79693 yrdC N (6)-threonylcarbamoyltransferase domain containing HCP5 Not_FC FC&PV -0.8 1.9 2.8 3.6 1.1 5.7 1.5 3.6 1.2 10866 HLA complex P5 (non-protein coding) RALGDS Not_FC FC&PV -0.7 0.7 2.4 1.7 0.7 5.2 0.4 3.5 0.5 5900 ral guanine nucleotide dissociation stimulator ACLY Not_FC FC&PV -0.6 0.7 2.3 1.4 0.7 6.3 0.6 4.5 0.5 CN -1.8 47 ATP citrate lyase TMEM177 Not_FC FC&PV -0.7 0.4 2.2 0 0.4 6 0.5 2.4 0.5 80775 transmembrane protein 177 STON1 Not_FC FC&PV 0.8 -1.8 2.1 0 0.7 6.4 1.3 2.5 1 11037 stonin 1 CYB561 Not_FC FC&PV -0.6 0.6 2.1 1.3 1.1 6.5 0.6 4.5 0.7 1534 b561 DHPS Not_FC FC&PV -0.8 1.9 2 1.5 1.2 6.5 0.7 5.5 0.7 1725 deoxyhypusine synthase ARL4C Not_FC FC&PV -0.8 1.1 2 1.6 0.5 6.6 1.2 5 1.5 10123 ADP-ribosylation factor-like 4C CYFIP2 Not_FC Not -0.7 -0.7 2.3 0.1 0.2 5.6 0.7 3 0.7 26999 cytoplasmic FMR1 interacting protein 2 ANKRD28 Not_FC RNAseq_only -0.5 9.7 0.3 2.8 0.5 23243 ankyrin repeat domain 28 MRPS28 Not_FC RNAseq_only 0.7 3.7 0.5 5.1 0.6 28957 mitochondrial ribosomal protein S28 SKIL Not_FC RNAseq_only -0.7 2.8 0.5 3.2 0.9 CN 3.5 6498 SKI-like proto-oncogene FAH Not_FC&PV FC -0.8 1.6 3 0 3.3 5.1 0.8 2.2 0.8 2184 fumarylacetoacetate (fumarylacetoacetase) API5 Not_FC&PV FC 1 -0.7 2.8 0 1.5 6 0.5 4.8 0.5 8539 apoptosis inhibitor 5 CDC123 Not_FC&PV FC 0.8 -0.4 2.7 0.2 2.3 8.1 0.6 5.2 0.4 8872 cell division cycle 123 TMPRSS3 Not_FC&PV FC -0.8 1.8 2.7 0 2.5 7.7 1.1 4.7 0.9 64699 transmembrane protease, serine 3 MTCH2 Not_FC&PV FC 1 -1.4 2.6 0 1.6 8.4 0.5 5.2 0.4 23788 mitochondrial carrier 2 BCL2L13 Not_FC&PV FC -0.6 2 2.1 0 10.2 5.5 0.6 3.1 0.4 23786 BCL2-like 13 (apoptosis facilitator) C5orf22 Not_FC&PV FC -0.6 0.8 2.1 0.8 1.8 6.9 0.5 3.6 0.4 55322 chromosome 5 open reading frame 22 RASSF9 Not_FC&PV FC&PV 1 -1.4 3 0 3.2 5.8 1 2.8 0.9 9182 Ras association (RalGDS/AF-6) domain family member 9 PSME2 Not_FC&PV FC&PV -0.6 0.6 2 1.4 1.7 9.5 0.6 7 0.8 -1.7 5721 proteasome activator subunit 2 HPSE NA FC&PV 0.9 2.3 0 5.5 1.2 2.4 1.1 10855 heparanase PRKCQ NA FC&PV 0.7 2.1 0 5.6 1 2.5 0.8 5588 C, theta TTC30A NA FC&PV -0.7 2 4.8 5 0.7 2.4 0.7 92104 tetratricopeptide repeat domain 30A RPL23AP82 NA Not 0.8 3.1 0 5.3 0.6 1.4 0.4 284942 ribosomal protein L23a pseudogene 82 LOC90784 NA RNAseq_only 4 2.5 0.7 CN -1.9 90784 uncharacterized LOC90784 RECQL5 NA RNAseq_only 4 2.5 0.5 CN -1.6 9400 RecQ -like 5 HOXD8 NA RNAseq_only 3.7 3.3 1.3 3234 homeobox D8 CST1 NA RNAseq_only 3.5 2.3 1.9 1469 cystatin SN CTBP1-AS2 NA RNAseq_only 3.2 2.5 0.6 92070 CTBP1 antisense RNA 2 (head to head) HSPB2 NA RNAseq_only 3.2 2.5 1 3316 heat shock 27kDa protein 2 MTOR NA RNAseq_only 2.2 3.2 0.6 CN 1.4 2475 mechanistic target of rapamycin (serine/threonine kinase) PRKAR1A Not FC -0.9 3.3 0 7.9 0.6 5.1 0.5 CN -1.4 5573 protein kinase, cAMP-dependent, regulatory, type I, alpha ADGRL1 Not FC -0.7 3.2 0.8 5.2 0.8 3.8 1.1 22859 adhesion G protein-coupled receptor L1 ARFGAP2 Not FC 0.8 3 0 6.6 0.5 4.2 0.4 84364 ADP-ribosylation factor GTPase activating protein 2 PPIE Not FC 1 2.9 1.1 5.4 0.5 3.2 0.5 CN 1.6 10450 peptidylprolyl E (cyclophilin E) MEAF6 Not FC 1.1 2.8 1.1 8.2 0.6 5 0.5 1.3 64769 MYST/Esa1-associated factor 6 PLSCR4 Not FC 0.8 2.7 0.9 6.2 1.1 3 1.1 57088 phospholipid scramblase 4 UCP2 Not FC -0.9 2.6 1 9.1 0.8 8.3 1 7351 uncoupling protein 2 (mitochondrial, proton carrier) TCFL5 Not FC 0.7 2.5 0.4 6.5 0.8 2.6 0.6 CN_FC_oposite-2.3 10732 transcription factor-like 5 (basic helix-loop-helix) KLC1 Not FC -0.7 2.5 0 6.1 0.5 3.5 0.4 3831 light chain 1 PRDX2 Not FC -0.8 2.5 1.2 10.2 0.7 8.1 0.9 7001 peroxiredoxin 2 ADCK3 Not FC 0.5 2.4 1.2 6.9 0.6 3.5 0.5 CN_FC_oposite-1.6 56997 aarF domain containing kinase 3 NPDC1 Not FC -0.5 2.4 1.1 5.4 0.9 3.8 1.1 56654 neural proliferation, differentiation and control, 1 ECHDC3 Not FC 0.8 2.3 0.4 6.4 0.9 4 0.7 79746 enoyl CoA hydratase domain containing 3 TK1 Not FC -0.8 2.3 1.2 5.7 0.8 5.5 1 -1.8 7083 1, soluble KBTBD4 Not FC 0.9 2.2 0 5.8 0.5 3.5 0.4 55709 kelch repeat and BTB (POZ) domain containing 4 BCKDHA Not FC 0.8 2.2 0.9 6.7 0.9 5 0.7 593 branched chain keto acid dehydrogenase E1, alpha polypeptide GPSM2 Not FC 0.8 2.2 0.6 5.9 0.7 3 0.5 29899 G-protein signaling modulator 2 GNL2 Not FC 0.7 2.2 1.2 8.1 0.6 4.9 0.6 1.3 29889 guanine nucleotide binding protein-like 2 (nucleolar) DFFA Not FC 0.6 2.1 1.3 7.1 0.6 3.9 0.5 CN 1.7 1676 DNA fragmentation factor, 45kDa, alpha polypeptide SYNGR2 Not FC -0.6 2.1 1.1 8.5 0.7 7.4 0.7 -1.8 9144 synaptogyrin 2 GALNS Not FC -0.6 2.1 0.5 5.6 0.7 3.2 0.7 2588 galactosamine (N-acetyl)-6-sulfatase C5orf15 Not FC -0.7 2.1 0.7 8.5 0.5 5.5 0.5 56951 chromosome 5 open reading frame 15 PPP1R10 Not FC -0.6 2 0 6 0.5 4.2 0.4 5514 protein phosphatase 1, regulatory subunit 10 SATB1 Not FC -0.6 2 0 5.7 1 1.5 0.7 6304 SATB homeobox 1 HIVEP1 Not FC&PV 0.9 3.4 0 5.8 0.6 2.4 0.6 3096 human immunodeficiency virus type I enhancer binding protein 1 CYB561D2 Not FC&PV -0.9 3.4 1.9 5.5 0.6 3.4 0.6 11068 cytochrome b561 family, member D2 SPA17 Not FC&PV -0.9 3.1 3.2 5.9 1 3.7 0.9 53340 sperm autoantigenic protein 17 IPO4 Not FC&PV -0.9 3 1.8 6 0.6 4.8 0.5 CN -1.7 79711 importin 4 RRAGC Not FC&PV 0.9 2.9 1.5 7.8 0.7 3.7 0.5 CN 2.3 64121 Ras-related GTP binding C PHKA2 Not FC&PV 0.8 2.8 1.7 6 0.7 2.9 0.6 5256 kinase, alpha 2 (liver) THTPA Not FC&PV -1 2.7 3.5 6.4 0.7 3.4 0.7 CN -1.4 79178 thiamine triphosphatase C9orf116 Not FC&PV -0.8 2.6 1.8 5.2 0.7 3 0.9 138162 open reading frame 116 CNP Not FC&PV -1 2.6 0 7.1 0.5 4.1 0.4 CN -2 1267 2',3'-cyclic nucleotide 3' phosphodiesterase APPL1 Not FC&PV 0.8 2.5 0 6.1 0.8 3.4 0.5 26060 adaptor prot, phosphotyrosine interaction, PH dom leucine zipper 1 GTF3C3 Not FC&PV 1.1 2.5 2.1 6.8 0.7 3.6 0.6 9330 general transcription factor IIIC, polypeptide 3, 102kDa LTBP2 Not FC&PV 0.7 2.5 2.7 7.5 1.1 3.8 1.1 4053 latent transforming growth factor beta binding protein 2 TOR1A Not FC&PV -0.7 2.5 0 6.5 0.5 3.8 0.4 1861 torsin family 1, member A (torsin A) MRPL24 Not FC&PV -1 2.4 3.4 8.8 0.6 6.4 0.7 79590 mitochondrial ribosomal protein L24 AGTPBP1 Not FC&PV 1 2.4 0 5.5 0.6 1.9 0.5 23287 ATP/GTP binding protein 1 RAD23A Not FC&PV -0.7 2.3 1.3 8.2 0.6 7.3 0.6 5886 RAD23 homolog A, nucleotide excision repair protein PDZD2 Not FC&PV 0.8 2.2 0 5.9 1.1 1.8 0.8 23037 PDZ domain containing 2 NUP98 Not FC&PV 0.8 2.2 2.3 5.5 0.5 3.9 0.5 CN 2.8 4928 nucleoporin 98kDa DEAF1 Not FC&PV 1 2.2 1.4 5.3 0.7 4 0.7 CN 2.4 10522 DEAF1 transcription factor MBIP Not FC&PV -0.7 2.2 2 5.5 0.6 3.9 0.6 -1.3 51562 MAP3K12 binding inhibitory protein 1 ACTR10 Not FC&PV -0.8 2.2 0 8.8 0.7 4.2 0.4 55860 actin-related protein 10 homolog (S. cerevisiae) CSNK1D Not FC&PV -0.7 2.1 0 6.6 0.5 4.7 0.4 CN -2.5 1453 , delta ATP9A Not FC&PV -0.8 2.1 2.5 7.5 0.7 3.8 0.7 CN -6.5 10079 ATPase, class II, type 9A MYNN Not FC&PV 1.1 2.1 2.5 6.3 0.7 3.7 0.6 CN 3.1 55892 myoneurin GMPR2 Not FC&PV -0.7 2.1 3.1 6.6 0.7 4.1 0.5 CN -1.7 51292 guanosine monophosphate reductase 2 GALT Not FC&PV -0.7 2.1 1.9 5.3 0.6 3.3 0.6 2592 galactose-1-phosphate uridylyltransferase MGMT Not FC&PV -0.8 2.1 1.8 6.5 0.7 4.6 0.8 4255 O-6-methylguanine-DNA methyltransferase NIT1 Not FC&PV -0.8 2.1 0 6.6 0.6 3.8 0.4 4817 nitrilase 1 CTR9 Not FC&PV 0.6 2 0 6.9 0.8 3.4 0.5 CN 2.2 9646 CTR9 homolog, Paf1/RNA polymerase II complex component C19orf54 Not FC&PV 0.8 2 1.7 6.3 0.8 3.2 0.7 284325 open reading frame 54 SLC35A1 Not Not 0.6 2.2 0.1 7.4 0.7 3 0.6 10559 solute carrier family 35 (CMP-sialic acid transporter), mem A1 ZCCHC6 Not Not -0.7 2 0 6 0.7 1.6 0.4 CN 1.5 79670 zinc finger, CCHC domain containing 6 MRPL52 Not RNAseq_only 4.7 5 0.9 CN -1.9 122704 mitochondrial ribosomal protein L52 C4orf48 Not RNAseq_only 4.2 4.9 1.4 401115 chromosome 4 open reading frame 48 SLC25A25 Not RNAseq_only 3.9 2.5 0.8 114789 solute carrier family 25 C11orf52 Not RNAseq_only 3.6 3.1 0.8 91894 chromosome 11 open reading frame 52 ERAP1 Not RNAseq_only 3.1 3.3 0.8 51752 aminopeptidase 1 CHMP6 Not RNAseq_only 2.9 4 0.6 CN -1.9 79643 charged multivesicular body protein 6 URB1-AS1 Not RNAseq_only 2.8 3.3 0.7 84996 URB1 antisense RNA 1 (head to head) SRC Not RNAseq_only 2.7 3.7 0.8 CN -2 6714 SRC proto-oncogene, non-receptor FANCF Not_relevant Not_relevant -0.2 0.3 0.6 6 0.7 3 0.5 2188 Fanconi anemia, complementation group F ATM Not_relevant Not_relevant -0.6 -2.4 1.4 0 1 5.1 0.6 1.5 0.5 472 ATM serine/threonine kinase

Abbreviations: FC&PV validated by p<0.05 and consistent Fold Change FC validated by consistent Fold Change Not Not validated: p>0.05 and abs(Fold Change)<0.4 Not_FC&PV Not validated and p<0.05 and inconsistent Fold Change Not_FC Not validated and inconsistent Fold Change RNAseq_only absent on Affymetrix array Not_relevant was included for some other reason NA Not available CN p<0.05 difference in average Copy numbers and consistent Fold Change CN_FC_oposite p<0.05 difference in average Copy numbers and inconsistent Fold Change

Columns: GeneID Hugo Symbol Validation_Inhouse summary for In-house cohort Validation_TCGA_RNAseq summary for RNA-seq TCGA log10PValue_TCGA_Affy_Normalized t-test 17 CDK12 TD-plus phenotype versus 57 reference samples TCGA Affymetrix platform filtered and normalized values log10PValue_TCGA_RNAseq_Normalized t-test 13 CDK12 TD-plus phenotype versus 56 reference samples TCGA RNA-seq platform filtered and normalized values FoldChange_TCGA_Affy_Normalized 17 CDK12 TD-plus phenotype versus 57 reference samples TCGA Affymetrix platform filtered and normalized values log10PValue_Affy_InHouse_Raw t-test 3 CDK12 TD-plus phenotype versus 33 other cases Inhouse Affymetrix platform FoldChange_Affy_InHouse_Raw 3 CDK12 TD-plus phenotype versus 33 other cases Inhouse Affymetrix platform Mean_TCGA_Affy mean value for 74 cases included into t-test comparison TCGA Affymetrix platform SD_TCGA_Affy standard deviation for 74 cases included into t-test comparison TCGA Affymetrix platform Mean_TCGA_RNAseq mean value for 70 cases included into t-test comparison TCGA RNA-seq SD_TCGA_RNAseq standard deviation for 70 cases included into t-test comparison TCGA RNA-seq Confounding_CN CN indicates that the gene has p<0.05 different relative copy numbers in CDK12 TD-plus phenotype tumors compared to the reference samples log10PValue_TCGA_RNAseq_CN t-test for relative copy numbers (sign corresponds to the fold change derection) in CDK12 TD-plus phenotype tumors versus the reference samples Gene ID DESCRIPTION Gene description