Supplementary file 1B. Differentially expressed genes in cancers compared to non-cancers, ranked according to statistical significance based on features present in all samples in at least one replicate. Acc UGCluster Name Symbol log Fold Changet Adj. P - Value B T57841 Hs.474213 Ubiquitin fusion degradation 1 like (yeast) UFD1L 5,02 5,77E-17 36,61 AA279072 Hs.523875 Inositol polyphosphate phosphatase-like 1 INPPL1 4,29 3,40E-16 34,34 AA454143 Hs.77500 Ubiquitin specific peptidase 4 (proto-oncogene) USP4 5,47 9,11E-16 33,04 N68327 Hs.675604 Transcribed locus 5,16 1,33E-15 32,42 T47230 Hs.522885 Zinc finger protein 32 ZNF32 4,96 3,20E-15 31,39 N95249 Hs.505033 V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog KRAS 5,90 1,30E-14 29,85 R41787 Data not found 3,94 1,30E-14 29,75 H51262 Hs.658489 Chloride channel CLIC-like 1 CLCC1 5,67 3,80E-14 28,60 N74623 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 8,04 1,04E-13 27,52 AA001614 Data not found 6,13 1,97E-13 26,81 AA488626 Hs.81424 SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae) SUMO1 6,74 2,96E-13 26,33 N50854 Hs.534334 Nucleolar protein 1, 120kDa NOL1 7,55 4,20E-13 25,91 N54596 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 6,47 5,33E-12 23,37 AA129397 Hs.522868 Deleted in azoospermia 1 DAZ1 2,09 2,37E-11 21,85 N54596 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 6,58 2,37E-11 21,78 AA424871 Hs.236646 Transcribed locus 3,00 2,11E-10 19,59 AA446876 Hs.165950 Fibroblast growth factor receptor 4 FGFR4 1,93 5,48E-10 18,59 AA152347 Hs.485557 Glutathione S-transferase A4 GSTA4 -2,38 1,31E-09 17,68 AA598863 Hs.535464 Eukaryotic translation initiation factor 3, subunit C-like EIF3CL 2,02 1,86E-09 17,28 H66005 Data not found 3,87 2,30E-09 17,03 AA677246 Data not found -1,74 3,20E-09 16,65 N47484 Hs.485557 Glutathione S-transferase A4 GSTA4 -2,36 3,50E-09 16,52 AI365391 Hs.153357 Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 PLOD3 1,52 5,02E-09 16,09 AA150422 Hs.221941 Cytochrome b reductase 1 CYBRD1 -2,56 5,02E-09 16,08 AA664101 Hs.76392 Aldehyde dehydrogenase 1 family, member A1 ALDH1A1 -2,87 6,82E-09 15,74 N20305 Hs.20575 Growth arrest-specific 2 like 3 GAS2L3 2,00 9,23E-09 15,40 AA211761 Hs.598634 Transcribed locus -1,69 1,28E-08 15,02 AA482067 Hs.647064 Retinoic acid receptor responder (tazarotene induced) 2 RARRES2 -2,20 1,28E-08 15,00 H77536 Hs.497469 Ethanolamine kinase 2 ETNK2 2,09 1,71E-08 14,68 R70784 Hs.102696 Malignant T cell amplified sequence 1 MCTS1 1,30 1,82E-08 14,59 H01164 Hs.268887 MRNA; cDNA DKFZp686P05119 (from clone DKFZp686P05119) 1,25 1,82E-08 14,56 AA948055 Hs.349283 Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CBX5 1,51 1,84E-08 14,52 AA863125 Hs.112981 DEP domain containing 6 DEPDC6 -1,95 2,02E-08 14,39 AA865224 Hs.709396 Homo sapiens, clone IMAGE:4096273, mRNA -1,30 2,02E-08 14,37 AA858223 Hs.144447 Bromodomain and WD repeat domain containing 2 BRWD2 1,54 2,23E-08 14,24 W49619 Hs.464829 Cadherin 2, type 1, N-cadherin (neuronal) CDH2 -3,06 2,28E-08 14,19 AA417905 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,76 2,61E-08 14,03 AA936302 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,80 2,81E-08 13,93 R20737 Hs.73625 Kinesin family member 20A KIF20A 1,12 2,88E-08 13,88 H96878 Hs.709414 Transmembrane emp24 protein transport domain containing 4 TMED4 1,10 2,92E-08 13,84 T63980 Hs.632994 MRNA differentially expressed in malignant melanoma, clone MM D3 1,68 3,12E-08 13,75 H19129 Hs.584758 Fibroblast growth factor 12 FGF12 -2,72 3,62E-08 13,58 N69220 Hs.480848 Ubiquitin specific peptidase 38 USP38 1,07 4,13E-08 13,43 R41227 Hs.203965 Putative homeodomain transcription factor 2 PHTF2 1,12 4,85E-08 13,24 AA670419 Hs.592207 Chromosome 22 open reading frame 9 C22orf9 -1,10 4,85E-08 13,22 W67200 Hs.334587 RNA binding protein with multiple splicing RBPMS -1,19 4,98E-08 13,18 W80761 Hs.435413 Metastasis associated 1 family, member 3 MTA3 -1,29 5,27E-08 13,10 AA488297 Hs.595186 Transcribed locus 1,04 5,49E-08 13,04 H90902 Hs.153546 Cell division cycle 23 homolog (S. cerevisiae) CDC23 1,13 8,51E-08 12,58 H17615 Hs.332708 Fibulin 5 FBLN5 -2,56 8,80E-08 12,53 AA199717 Hs.101174 Microtubule-associated protein tau MAPT 1,10 1,17E-07 12,23 AA430504 Hs.93002 Ubiquitin-conjugating enzyme E2C UBE2C 1,53 1,23E-07 12,17 H21943 Data not found 1,76 1,25E-07 12,12 H14208 Hs.631841 Paralemmin PALM -1,44 1,33E-07 12,05 H56345 Hs.709539 Chromosome 19 open reading frame 59 C19orf59 2,64 1,35E-07 12,02 AA490462 Hs.439463 AE binding protein 1 AEBP1 -1,37 1,38E-07 11,97 AA991590 Hs.110675 Apolipoprotein C-I APOC1 -3,26 1,75E-07 11,73 R17667 Hs.706748 Solute carrier family 2 (facilitated glucose transporter), member 1 SLC2A1 1,95 1,99E-07 11,58 H44785 Hs.714159 Transcribed locus 1,23 5,36E-07 10,35 AA004881 Hs.440401 Retinol saturase (all-trans-retinol 13,14-reductase) RETSAT -1,14 5,36E-07 10,34 N30428 Hs.122926 Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid rece NR3C1 0,80 5,36E-07 10,33 AA873159 Hs.110675 Apolipoprotein C-I APOC1 -3,22 5,79E-07 10,24 R54846 Hs.264887 Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfe FGFR1 1,45 5,88E-07 10,22 H20543 Hs.6278 Dihydroxyacetone kinase 2 homolog (S. cerevisiae) DAK -1,81 5,98E-07 10,18 R78586 Hs.7753 Transcribed locus 1,27 5,98E-07 10,17 AA034051 Hs.158932 Adenomatous polyposis coli APC 1,05 5,98E-07 10,16 AA873599 Hs.460960 Iduronate 2-sulfatase (Hunter syndrome) IDS 1,61 6,07E-07 10,13 R39446 Hs.714136 Transcribed locus -2,08 6,08E-07 10,12 R85914 Hs.437993 MAM domain containing glycosylphosphatidylinositol anchor 1 MDGA1 1,75 6,25E-07 10,08 R72507 Data not found 0,91 6,32E-07 10,06 H59625 Hs.560373 Transcribed locus 1,27 6,38E-07 10,04 AA142922 Hs.655143 Sorbin and SH3 domain containing 2 SORBS2 -3,04 6,39E-07 10,03 AA598601 Hs.697535 Insulin-like growth factor binding protein 3 IGFBP3 2,15 6,65E-07 9,98 H48148 Hs.4944 Chromosome 9 open reading frame 58 C9orf58 1,91 7,03E-07 9,91 AA443702 Hs.707333 Transcribed locus 1,00 7,16E-07 9,88 H10713 Data not found 1,25 7,28E-07 9,85 N21334 Hs.471156 Abl interactor 2 ABI2 -0,92 7,45E-07 9,82 R42227 Hs.245791 Transcribed locus 0,94 7,90E-07 9,74 R55993 Data not found -1,03 7,90E-07 9,74 R06900 Data not found 1,52 8,21E-07 9,69 R42112 Hs.513856 Candidate tumor suppressor in ovarian cancer 2 DPH1 1,03 8,67E-07 9,63 AA465389 Hs.474781 Neutrophil cytosolic factor 4, 40kDa NCF4 -1,22 8,96E-07 9,58 AA453512 Hs.521954 Transcribed locus, strongly similar to NP_036211.2 diacylglycerol O-acyltransfera -1,21 9,73E-07 9,49 AA521300 Hs.333297 Speckle-type POZ protein-like SPOPL 2,40 1,05E-06 9,41 R33642 Hs.523836 Glutathione S-transferase pi GSTP1 -1,72 1,05E-06 9,39 AA479202 Hs.644633 TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy, pseudoin TIMP3 -2,12 1,17E-06 9,28 H58873 Hs.706748 Solute carrier family 2 (facilitated glucose transporter), member 1 SLC2A1 1,86 1,20E-06 9,24 H22922 Hs.517603 MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase MFNG -1,09 1,20E-06 9,23 R09561 Hs.527653 CD55 molecule, decay accelerating factor for complement (Cromer blo CD55 -1,80 1,37E-06 9,10 R44870 Hs.369606 Cleavage and polyadenylation specific factor 6, 68kDa CPSF6 -1,00 1,48E-06 9,01 AA829294 Hs.437855 RNA polymerase II associated protein 3 RPAP3 1,02 1,88E-06 8,76 AA426516 Hs.645557 Transcribed locus 1,32 1,90E-06 8,74 W74133 Hs.47125 GINS complex subunit 3 (Psf3 homolog) GINS3 1,13 1,97E-06 8,70 AA449715 Hs.15154 Sushi-repeat-containing protein, X-linked SRPX -1,29 2,10E-06 8,63 N95578 Hs.535801 CDNA clone IMAGE:4346813 1,04 2,25E-06 8,55 AA485893 Hs.78224 Ribonuclease, RNase A family, 1 (pancreatic) RNASE1 -2,26 2,30E-06 8,52 R33439 Hs.24640 Semaphorin 7A, GPI membrane anchor (John Milton Hagen blood grou SEMA7A 1,20 2,30E-06 8,50 AA701963 Hs.521212 Aldo-keto reductase family 1, member B1 (aldose reductase) AKR1B1 -2,69 2,30E-06 8,50 N54296 Hs.94949 Methylmalonyl CoA epimerase MCEE -0,74 2,30E-06 8,49 R56149 Hs.533336 BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) BAMBI -1,00 2,30E-06 8,49 H14810 Data not found 1,43 2,32E-06 8,47 AA461071 Hs.516866 Solute carrier family 23 (nucleobase transporters), member 2 SLC23A2 -1,81 2,36E-06 8,44 W74668 Hs.59138 Glycophorin C (Gerbich blood group) GYPC -1,21 2,39E-06 8,42 H81645 Hs.162877 Protein kinase C and casein kinase substrate in neurons 2 PACSIN2 -1,18 2,54E-06 8,35 R55294 Data not found -1,82 2,65E-06 8,30 AA457728 Data not found 1,01 2,80E-06 8,24 AA406231 Hs.712560 Dishevelled associated activator of morphogenesis 2 DAAM2 -2,09 2,81E-06 8,23 AA465381 Hs.632527 Solute carrier family 35, member F5 SLC35F5 -1,11 3,02E-06 8,15 AA451851 Hs.102735 Single-stranded DNA binding protein 2 SSBP2 1,47 3,18E-06 8,09 AI361330 Hs.469030 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, me MTHFD2 1,15 3,23E-06 8,06 AA465663 Hs.654395 Fc fragment of IgG, low affinity IIb, receptor (CD32) FCGR2B -1,08 3,23E-06 8,05 H98241 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,84 3,23E-06 8,05 R07607 Hs.349283 Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CBX5 0,99 3,48E-06 7,97 N48827 Hs.467524 Ubiquitin specific peptidase 48 USP48 -1,16 3,50E-06 7,96 R51912 Hs.12409 Somatostatin SST 0,93 3,51E-06 7,95 T72259 Data not found 1,59 3,51E-06 7,94 AA683321 Hs.664675 Prader-Willi/Angelman syndrome-5 PAR5 1,29 3,51E-06 7,93 R07296 Hs.496383 Sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferas SOAT1 -1,72 3,75E-06 7,86 AA678159 Hs.563228 Transcribed locus -2,13 3,76E-06 7,85 AA757678 Data not found 1,17 8,09E-06