Supplemental Digital Content 2 List of down-regulated transcripts in colonic mucosal UC-associated dysplasia and pancolitis compared to left-sided colitis Probe Set ID Gene Title Gene Symbol 225655_at ubiquitin-like, containing PHD and RING finger domains, 1 UHRF1 216640_s_at protein disulfide isomerase family A, member 6 PDIA6 1555358_a_at ectonucleoside triphosphate diphosphohydrolase 4 ENTPD4 201340_s_at ectodermal-neural cortex (with BTB-like domain) ENC1 203843_at ribosomal protein S6 kinase, 90kDa, polypeptide 3 RPS6KA3 206668_s_at secretory carrier membrane protein 1 SCAMP1 207791_s_at RAB1A, member RAS oncogene family RAB1A 228996_at roquin KIAA2025 Transcribed locus, weakly similar to XP_517454.1 PREDICTED: 228623_at similar to hypothetical protein MGC45438 [Pan troglodytes] --- 202817_s_at synovial sarcoma translocation, chromosome 18 SS18 235234_at hypothetical protein FLJ36874 FLJ36874 201514_s_at Ras-GTPase-activating protein SH3-domain-binding protein G3BP 218238_at GTP binding protein 4 GTPBP4 241343_at Ribonuclease H1 RNASEH1 1553033_at synaptotagmin-like 5 SYTL5 203210_s_at replication factor C (activator 1) 5, 36.5kDa RFC5 213875_x_at chromosome 6 open reading frame 62 C6orf62 1553108_at hypothetical protein FLJ37562 FLJ37562 215820_x_at sorting nexin 13 SNX13 230130_at Slit homolog 2 (Drosophila) SLIT2 200607_s_at RAD21 homolog (S. pombe) RAD21 235296_at eukaryotic translation initiation factor 5A2 EIF5A2 1552656_s_at U2AF homology motif (UHM) kinase 1 UHMK1 214155_s_at La ribonucleoprotein domain family, member 4 LARP4 203328_x_at insulin-degrading enzyme IDE 214962_s_at nucleoporin 160kDa NUP160 236327_at Hypothetical protein FLJ22457 FLJ22457 1564064_a_at ATPase, Class VI, type 11B ATP11B 223785_at hypothetical protein FLJ10719 FLJ10719 212392_s_at phosphodiesterase 4D interacting protein (myomegalin) PDE4DIP LOC163131 /// 215570_s_at hypothetical BC331191_1 /// hypothetical protein LOC284323 LOC284323 210188_at GA binding protein transcription factor, alpha subunit 60kDa GABPA 1552921_a_at fidgetin-like 1 FIGNL1 211536_x_at mitogen-activated protein kinase kinase kinase 7 MAP3K7 222977_at surfeit 4 SURF4 1553565_s_at dimethylarginine dimethylaminohydrolase 1 DDAH1 1554145_a_at smooth muscle myosin heavy chain 11 isoform SM1-like LOC129285 217230_at villin 2 (ezrin) VIL2 219911_s_at solute carrier organic anion transporter family, member 4A1 SLCO4A1 229553_at phosphoglucomutase 2-like 1 PGM2L1 208097_s_at thioredoxin domain containing /// thioredoxin domain containing TXNDC 218156_s_at hypothetical protein FLJ10534 FLJ10534 238644_at --- --- 241938_at Quaking homolog, KH domain RNA binding (mouse) QKI 209941_at receptor (TNFRSF)-interacting serine-threonine kinase 1 RIPK1 216205_s_at mitofusin 2 MFN2 213742_at splicing factor, arginine/serine-rich 11 SFRS11 1565717_s_at fusion (involved in t(12;16) in malignant liposarcoma) FUS 235088_at hypothetical protein LOC201725 LOC201725 203619_s_at Fas apoptotic inhibitory molecule 2 FAIM2 207379_at EGF-like repeats and discoidin I-like domains 3 EDIL3 224657_at mitogen-inducible gene 6 MIG-6 201295_s_at WD repeat and SOCS box-containing 1 WSB1 222583_s_at nucleoporin 50kDa NUP50 240983_s_at cysteinyl-tRNA synthetase CARS 211537_x_at mitogen-activated protein kinase kinase kinase 7 MAP3K7 223220_s_at poly (ADP-ribose) polymerase family, member 9 PARP9 201695_s_at nucleoside phosphorylase NP 226085_at Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CBX5 transforming growth factor, beta receptor I (activin A receptor type II- 206943_at like kinase, 53kDa) TGFBR1 220202_s_at membrane associated DNA binding protein MNAB 207686_s_at caspase 8, apoptosis-related cysteine protease CASP8 Eukaryotic translation elongation factor 1 delta (guanine nucleotide 213087_s_at exchange protein) EEF1D 1554433_a_at zinc finger protein 146 ZNF146 202647_s_at neuroblastoma RAS viral (v-ras) oncogene homolog NRAS 231819_at CCAAT/enhancer binding protein zeta CEBPZ 217356_s_at phosphoglycerate kinase 1 PGK1 1554249_a_at zinc finger protein 638 ZNF638 211015_s_at heat shock 70kDa protein 4 HSPA4 236223_s_at Transcribed locus --- 216202_s_at serine palmitoyltransferase, long chain base subunit 2 SPTLC2 1558034_s_at ceruloplasmin (ferroxidase) CP 201768_s_at enthoprotin ENTH 209052_s_at Wolf-Hirschhorn syndrome candidate 1 WHSC1 217138_x_at Immunoglobulin lambda variable 3-21 IGLC2 242727_at ADP-ribosylation factor-like 8 ARL8 202058_s_at karyopherin alpha 1 (importin alpha 5) KPNA1 204603_at exonuclease 1 EXO1 202613_at CTP synthase CTPS 1552627_a_at Rho GTPase activating protein 5 ARHGAP5 1554696_s_at thymidylate synthetase TYMS 215936_s_at KIAA1033 KIAA1033 1555337_a_at zinc finger protein 317 ZNF317 213022_s_at --- --- 232296_s_at G elongation factor, mitochondrial 1 GFM1 203769_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS 219868_s_at ankyrin repeat and FYVE domain containing 1 ANKFY1 220238_s_at kelch-like 7 (Drosophila) KLHL7 ADP-ribosylation factor guanine nucleotide-exchange factor 2 215931_s_at (brefeldin A-inhibited) ARFGEF2 211676_s_at interferon gamma receptor 1 /// interferon gamma receptor 1 IFNGR1 1555618_s_at SUMO-1 activating enzyme subunit 1 SAE1 231258_at --- --- 210458_s_at TRAF family member-associated NFKB activator TANK 209753_s_at thymopoietin TMPO 1559232_a_at Solute carrier family 33 (acetyl-CoA transporter), member 1 SLC33A1 238816_at Presenilin 1 (Alzheimer disease 3) PSEN1 205701_at importin 8 IPO8 phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole 212379_at synthetase GART 219927_at chromosome 14 open reading frame 111 C14orf111 208852_s_at calnexin CANX 212806_at KIAA0367 KIAA0367 Solute carrier family 28 (sodium-coupled nucleoside transporter), 232277_at member 3 SLC28A3 219691_at sterile alpha motif domain containing 9 SAMD9 1555972_s_at F-box protein 28 FBXO28 200664_s_at DnaJ (Hsp40) homolog, subfamily B, member 1 DNAJB1 205401_at alkylglycerone phosphate synthase AGPS 235744_at T-cell activation protein phosphatase 2C TA-PP2C 1555274_a_at selenoprotein I SELI 210405_x_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 235476_at tripartite motif-containing 59 TRIM59 223834_at CD274 antigen CD274 225931_s_at chromosome 17 open reading frame 27 C17orf27 229846_s_at mitogen-activated protein kinase associated protein 1 MAPKAP1 242458_at Ral GEF with PH domain and SH3 binding motif 2 RALGPS2 integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 1553530_a_at includes MDF2, MSK12) ITGB1 1553055_a_at hypothetical protein MGC19764 MGC19764 226825_s_at TPA regulated locus TPARL 212797_at sortilin 1 SORT1 low density lipoprotein receptor-related protein 8, apolipoprotein e 205282_at receptor LRP8 214505_s_at four and a half LIM domains 1 FHL1 217309_s_at Down syndrome critical region gene 3 DSCR3 238689_at G protein-coupled receptor 110 GPR110 212093_s_at mitochondrial tumor suppressor 1 MTUS1 227384_s_at Similar to KIAA0454 protein --- ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu 201727_s_at antigen R) ELAVL1 1558249_s_at syntaxin 16 STX16 227314_at Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) ITGA2 238563_at Trans-prenyltransferase TPRT 1552613_s_at CDC42 small effector 2 CDC42SE2 208459_s_at exportin 7 XPO7 1558647_at SH3 domain protein D19 SH3D19 223098_s_at peroxisomal lon protease LONP DKFZp434N2 228378_at hypothetical protein DKFZp434N2030 030 signal transducer and activator of transcription 3 (acute-phase 208992_s_at response factor) STAT3 207029_at KIT ligand KITLG 201171_at ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e ATP6V0E 1558959_at CDNA FLJ37917 fis, clone CTONG1000137 --- 210567_s_at S-phase kinase-associated protein 2 (p45) SKP2 218663_at chromosome condensation protein G HCAP-G 215708_s_at primase, polypeptide 2A, 58kDa PRIM2A 1554327_a_at calcium activated nucleotidase 1 CANT1 209162_s_at PRP4 pre-mRNA processing factor 4 homolog (yeast) PRPF4 200671_s_at spectrin, beta, non-erythrocytic 1 SPTBN1 223730_at glypican 6 GPC6 228459_at family with sequence similarity 84, member A FAM84A 217097_s_at putative homeodomain transcription factor 2 PHTF2 222679_s_at RP42 homolog RP42 transglutaminase 2 (C polypeptide, protein-glutamine-gamma- 211573_x_at glutamyltransferase) TGM2 201196_s_at adenosylmethionine decarboxylase 1 AMD1 1555334_s_at solute carrier family 30 (zinc transporter), member 5 SLC30A5 200790_at ornithine decarboxylase 1 ODC1 222611_s_at paraspeckle component 1 PSPC1 211968_s_at heat shock 90kDa protein 1, alpha HSPCA 228490_at abhydrolase domain containing 2 ABHD2 217014_s_at alpha-2-glycoprotein 1, zinc AZGP1 209023_s_at stromal antigen 2 STAG2 1554679_a_at lysosomal associated protein transmembrane 4 beta LAPTM4B 226094_at Phosphoinositide-3-kinase, class 2, alpha polypeptide PIK3C2A 241705_at ATP-binding cassette, sub-family A (ABC1), member 5 ABCA5 235643_at sterile alpha motif domain containing 9-like SAMD9L 224046_s_at phosphodiesterase 7A PDE7A 1554029_a_at KIAA0372 KIAA0372 1559038_at septin 2 SEPT2 1554441_a_at KIAA0261 KIAA0261 1555772_a_at cell division cycle 25A CDC25A 204716_at coiled-coil domain containing 6 CCDC6 phosphoribosylaminoimidazole carboxylase, 201014_s_at phosphoribosylaminoimidazole succinocarboxamide synthetase PAICS 202267_at laminin, gamma 2 LAMC2 protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), 202884_s_at beta isoform PPP2R1B 244563_at hypothetical protein FLJ21924 FLJ21924 203015_s_at synovial sarcoma, X breakpoint 2