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 Title Gene Symbol

225655_at ubiquitin-like, containing PHD and RING finger domains, 1 UHRF1 216640_s_at disulfide 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, 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 -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 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 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 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 interacting protein SSX2IP 242445_at FYVE, RhoGEF and PH domain containing 4 FGD4 202272_s_at F-box protein 28 FBXO28 220368_s_at KIAA2010 KIAA2010 222979_s_at surfeit 4 SURF4 212840_at KIAA0794 protein KIAA0794 239629_at CASP8 and FADD-like apoptosis regulator CFLAR 210023_s_at polycomb group ring finger 1 PCGF1 206113_s_at RAB5A, member RAS oncogene family RAB5A 224410_s_at limb region 1 homolog (mouse) /// limb region 1 homolog (mouse) LMBR1 206536_s_at baculoviral IAP repeat-containing 4 BIRC4 1559052_s_at p21 (CDKN1A)-activated kinase 2 PAK2 244030_at ------201539_s_at four and a half LIM domains 1 FHL1 ribulose-5-phosphate-3-epimerase /// similar to Ribulose-phosphate 3- RPE /// 216574_s_at epimerase (Ribulose-5-phosphate-3-epimerase) (HUSSY-17) LOC440001 233827_s_at suppressor of Ty 16 homolog (S. cerevisiae) SUPT16H 202719_s_at testis derived transcript (3 LIM domains) TES 203622_s_at putatative 28 kDa protein LOC56902 207724_s_at spastin SPAST 204770_at transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) TAP2 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation 200641_s_at protein, zeta polypeptide YWHAZ Protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform 229606_at (calcineurin A alpha) PPP3CA 215774_s_at ------238649_at phosphatidylinositol transfer protein, cytoplasmic 1 PITPNC1 213757_at Eukaryotic translation initiation factor 5A EIF5A 208934_s_at lectin, galactoside-binding, soluble, 8 (galectin 8) LGALS8 203764_at discs, large homolog 7 (Drosophila) DLG7 222922_at potassium voltage-gated channel, Isk-related family, member 3 KCNE3 213409_s_at Ras homolog enriched in brain RHEB 210052_s_at TPX2, microtubule-associated, homolog (Xenopus laevis) TPX2 230958_s_at Full length insert cDNA clone ZD69D05 --- 200841_s_at glutamyl-prolyl-tRNA synthetase EPRS 222600_s_at hypothetical protein FLJ10808 FLJ10808 205895_s_at nucleolar and coiled-body phosphoprotein 1 NOLC1 protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), 202886_s_at beta isoform PPP2R1B 232392_at Splicing factor, arginine/serine-rich 3 SFRS3 210649_s_at AT rich interactive domain 1A (SWI- like) ARID1A 1557984_s_at hypothetical protein FLJ21908 FLJ21908 203499_at EPH receptor A2 EPHA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) /// karyopherin 211762_s_at alpha 2 (RAG cohort 1, importin alpha 1) KPNA2 226661_at cell division cycle associated 2 CDCA2 210470_x_at non-POU domain containing, octamer-binding NONO 204989_s_at integrin, beta 4 ITGB4 207521_s_at ATPase, Ca++ transporting, ubiquitous ATP2A3 200879_s_at endothelial PAS domain protein 1 EPAS1 1555384_a_at La ribonucleoprotein domain family, member 4 LARP4 206364_at kinesin family member 14 KIF14 200041_s_at HLA-B associated transcript 1 /// HLA-B associated transcript 1 BAT1 207517_at laminin, gamma 2 LAMC2 209369_at annexin A3 ANXA3 1568592_at hypothetical gene supported by BC031266 LOC400368 203968_s_at CDC6 cell division cycle 6 homolog (S. cerevisiae) CDC6 214895_s_at a disintegrin and metalloproteinase domain 10 ADAM10 200831_s_at stearoyl-CoA desaturase (delta-9-desaturase) SCD 209624_s_at methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCCC2 214908_s_at transformation/transcription domain-associated protein TRRAP 232079_s_at poliovirus receptor-related 2 (herpesvirus entry mediator B) PVRL2 1555639_a_at RNA binding motif protein 14 RBM14 1559633_a_at cholinergic receptor, muscarinic 3 CHRM3 207782_s_at presenilin 1 (Alzheimer disease 3) PSEN1 215150_at YOD1 OTU deubiquinating enzyme 1 homolog ( yeast) YOD1 217496_s_at insulin-degrading enzyme IDE 219608_s_at F-box protein 38 FBXO38 chromosome 14 open reading frame 92 /// similar to Epidermal C14orf92 /// 217448_s_at Langerhans cell protein LCP1 LOC285412 210087_s_at myelin protein zero-like 1 MPZL1 203770_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS mitogen-activated protein kinase kinase kinase 2 /// mitogen-activated 221695_s_at protein kinase kinase kinase 2 MAP3K2 235189_at NMDA receptor regulated 2 NARG2 217881_s_at cell division cycle 27 CDC27 212332_at retinoblastoma-like 2 (p130) RBL2 210125_s_at barrier to autointegration factor 1 BANF1 212279_at hypothetical protein MAC30 MAC30 218800_at steroid 5 alpha-reductase 2-like SRD5A2L Mediator of RNA polymerase II transcription, subunit 28 homolog 214831_at (yeast) MED28 1554768_a_at MAD2 mitotic arrest deficient-like 1 (yeast) MAD2L1 heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor 216855_s_at A) HNRPU 203214_x_at cell division cycle 2, G1 to S and G2 to M CDC2 236191_at CD38 antigen (p45) CD38 212194_s_at transmembrane 9 superfamily protein member 4 TM9SF4 230492_s_at hypothetical protein KIAA1434 KIAA1434 238443_at Transcription factor A, mitochondrial TFAM 235574_at guanylate binding protein 4 GBP4 216684_s_at synovial sarcoma translocation, chromosome 18 SS18 227383_at Similar to KIAA0454 protein --- 1552516_a_at homeodomain interacting protein kinase 1 HIPK1 234989_at trophoblast-derived noncoding RNA TncRNA 211124_s_at KIT ligand KITLG 241706_at copine VIII CPNE8 238029_s_at solute carrier family 16 (monocarboxylic acid transporters), member 14 SLC16A14 200890_s_at signal sequence receptor, alpha (translocon-associated protein alpha) SSR1 213807_x_at met proto-oncogene (hepatocyte growth factor receptor) MET 201504_s_at translin TSN 216504_s_at Solute carrier family 39 (zinc transporter), member 8 SLC39A8 201946_s_at chaperonin containing TCP1, subunit 2 (beta) CCT2 205017_s_at muscleblind-like 2 (Drosophila) MBNL2 1554159_a_at zinc finger, MYND domain containing 11 ZMYND11 204768_s_at flap structure-specific endonuclease 1 FEN1 212720_at poly(A) polymerase alpha PAPOLA 207764_s_at homeodomain interacting protein kinase 3 HIPK3 1552978_a_at secretory carrier membrane protein 1 SCAMP1 204162_at kinetochore associated 2 KNTC2 1558733_at zinc finger and BTB domain containing 38 ZBTB38 208047_s_at NGFI-A binding protein 1 (EGR1 binding protein 1) NAB1 225754_at adaptor-related protein complex 1, gamma 1 subunit AP1G1 225186_at Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 RAPH1 226936_at chromosome 6 open reading frame 173 C6orf173 220955_x_at RAB23, member RAS oncogene family RAB23 208840_s_at Ras-GTPase activating protein SH3 domain-binding protein 2 G3BP2 218782_s_at ATPase family, AAA domain containing 2 ATAD2 212021_s_at antigen identified by monoclonal antibody Ki-67 MKI67 243431_at BTB (POZ) domain containing 14A BTBD14A proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; 209853_s_at Ki) PSME3 220295_x_at DEP domain containing 1 DEPDC1 201663_s_at SMC4 structural maintenance of 4-like 1 (yeast) SMC4L1 209678_s_at protein kinase C, iota PRKCI 209231_s_at dynactin 4 MGC3248 218295_s_at nucleoporin 50kDa NUP50 209872_s_at plakophilin 3 PKP3 240307_at Far upstream element (FUSE) binding protein 1 FUBP1 232112_at Ral GEF with PH domain and SH3 binding motif 2 RALGPS2 221218_s_at thiamin pyrophosphokinase 1 TPK1 203990_s_at ubiquitously transcribed tetratricopeptide repeat, UTX 200727_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 1553685_s_at Sp1 transcription factor SP1 214359_s_at heat shock 90kDa protein 1, beta HSPCB 222678_s_at RP42 homolog RP42 1553962_s_at ras homolog gene family, member B RHOB 211504_x_at Rho-associated, coiled-coil containing protein kinase 2 ROCK2 241425_at Nucleoporin like 1 NUPL1 200952_s_at cyclin D2 CCND2 212246_at multiple coagulation factor deficiency 2 MCFD2 1554152_a_at oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) OGDH 208698_s_at non-POU domain containing, octamer-binding NONO 209254_at KIAA0265 protein KIAA0265 202240_at polo-like kinase 1 (Drosophila) PLK1 1552612_at CDC42 small effector 2 CDC42SE2 1554334_a_at DnaJ (Hsp40) homolog, subfamily A, member 4 DNAJA4 234464_s_at essential meiotic endonuclease 1 homolog 1 (S. pombe) EME1 216627_s_at UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B4GALT1 241948_at Chromosome 9 open reading frame 42 C9orf42 227214_at golgi associated PDZ and coiled-coil motif containing GOPC 214697_s_at ROD1 regulator of differentiation 1 (S. pombe) ROD1 238635_at hypothetical protein FLJ21657 FLJ21657 1554333_at DnaJ (Hsp40) homolog, subfamily A, member 4 DNAJA4 207334_s_at transforming growth factor, beta receptor II (70/80kDa) TGFBR2 218542_at chromosome 10 open reading frame 3 C10orf3 241946_at zinc finger, DHHC-type containing 21 ZDHHC21 235016_at chromosome 10 open reading frame 74 C10orf74 229439_s_at RNA-binding protein FLJ20273 218073_s_at transmembrane protein 48 TMEM48 205446_s_at activating transcription factor 2 ATF2 222502_s_at ubiquitin-fold modifier 1 UFM1 204426_at coated vesicle membrane protein RNP24 234728_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 35 DHX35 235577_at Zinc finger protein 652 ZNF652 212009_s_at stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) STIP1 201308_s_at septin 11 SEPT11 214710_s_at cyclin B1 CCNB1 214513_s_at cAMP responsive element binding protein 1 CREB1 212022_s_at antigen identified by monoclonal antibody Ki-67 MKI67 219869_s_at solute carrier family 39 (zinc transporter), member 8 SLC39A8 221194_s_at PTD016 protein LOC51136 230609_at enthoprotin ENTH asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate 222556_at beta-glucosyltransferase) ALG5 214257_s_at SEC22 vesicle trafficking protein-like 1 (S. cerevisiae) SEC22L1 230333_at Spermidine/spermine N1-acetyltransferase SAT 204427_s_at coated vesicle membrane protein RNP24 234975_at G1 to S phase transition 1 GSPT1 220386_s_at echinoderm microtubule associated protein like 4 EML4 225088_at hypothetical protein FLJ31153 FLJ31153 212220_at proteasome (prosome, macropain) activator subunit 4 PSME4 219844_at chromosome 10 open reading frame 118 C10orf118 211814_s_at cyclin E2 CCNE2 224642_at forty-two-three domain containing 1 FYTTD1 222608_s_at anillin, actin binding protein (scraps homolog, Drosophila) ANLN 222393_s_at Mak3 homolog (S. cerevisiae) MAK3 223143_s_at chromosome 6 open reading frame 166 C6orf166 209642_at BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1 220153_at ectonucleoside triphosphate diphosphohydrolase 7 ENTPD7 207983_s_at stromal antigen 2 STAG2 222680_s_at denticleless homolog (Drosophila) DTL 217294_s_at enolase 1, (alpha) ENO1 209098_s_at jagged 1 (Alagille syndrome) JAG1 200712_s_at microtubule-associated protein, RP/EB family, member 1 MAPRE1 236293_at Ras homolog gene family, member H RHOH 209799_at protein kinase, AMP-activated, alpha 1 catalytic subunit PRKAA1 205394_at CHK1 checkpoint homolog (S. pombe) CHEK1 242963_at hypothetical protein MGC26963 MGC26963 223984_s_at nucleoporin like 1 NUPL1 200615_s_at adaptor-related protein complex 2, beta 1 subunit AP2B1 235331_x_at polycomb group ring finger 5 PCGF5 201992_s_at kinesin family member 5B KIF5B 205566_at abhydrolase domain containing 2 ABHD2 210732_s_at lectin, galactoside-binding, soluble, 8 (galectin 8) LGALS8 243786_at zinc finger, DHHC-type containing 20 ZDHHC20 211450_s_at mutS homolog 6 (E. coli) MSH6 201831_s_at vesicle docking protein p115 VDP sphingosine-1-phosphate phosphatase 1 /// sphingosine-1-phosphate 221268_s_at phosphatase 1 SGPP1 201337_s_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3 213016_at Bobby sox homolog (Drosophila) BBX v-ral simian leukemia viral oncogene homolog B (ras related; GTP 202101_s_at binding protein) RALB 231880_at family with sequence similarity 40, member B FAM40B NIMA (never in mitosis gene a)-related kinase 2 /// NIMA (never in 211080_s_at mitosis gene a)-related kinase 2 NEK2 233230_s_at KIAA1458 protein KIAA1458 239439_at AF4/FMR2 family, member 4 AFF4 1555434_a_at solute carrier family 39 (zinc transporter), member 14 SLC39A14 201686_x_at apoptosis inhibitor 5 API5 208744_x_at heat shock 105kDa/110kDa protein 1 HSPH1 218349_s_at Zwilch, kinetochore associated, homolog (Drosophila) ZWILCH 242422_at Ras-GTPase-activating protein SH3-domain-binding protein G3BP 1552610_a_at Janus kinase 1 (a protein tyrosine kinase) JAK1 212272_at lipin 1 LPIN1 234915_s_at density-regulated protein DENR 204109_s_at nuclear transcription factor Y, alpha NFYA 215253_s_at Down syndrome critical region gene 1 DSCR1 214008_at PTK9 protein tyrosine kinase 9 PTK9 240528_s_at SEC8-like 1 (S. cerevisiae) SEC8L1 platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 211547_s_at 45kDa PAFAH1B1 200832_s_at stearoyl-CoA desaturase (delta-9-desaturase) SCD 213562_s_at squalene epoxidase SQLE 211162_x_at stearoyl-CoA desaturase (delta-9-desaturase) SCD 235003_at U2AF homology motif (UHM) kinase 1 UHMK1 proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; 200987_x_at Ki) PSME3 Mediator of RNA polymerase II transcription, subunit 28 homolog 238761_at (yeast) MED28 225687_at chromosome 20 open reading frame 129 C20orf129 met proto-oncogene (hepatocyte growth factor receptor) /// met proto- 211599_x_at oncogene (hepatocyte growth factor receptor) MET 210818_s_at BTB and CNC homology 1, basic leucine zipper transcription factor 1 BACH1 228656_at Prospero-related homeobox 1 PROX1 224149_x_at sarcolemma associated protein SLMAP 200917_s_at signal recognition particle receptor ('docking protein') SRPR 1557078_at hypothetical protein MGC19764 MGC19764 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 209896_s_at 1) PTPN11 209629_s_at nuclear transport factor 2-like export factor 2 NXT2 1554390_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 201647_s_at scavenger receptor class B, member 2 SCARB2 201890_at ribonucleotide reductase M2 polypeptide RRM2 200722_s_at membrane component, chromosome 11, surface marker 1 M11S1 222387_s_at vacuolar protein sorting 35 (yeast) VPS35 Alport syndrome, mental retardation, midface hypoplasia and 1553219_a_at elliptocytosis chromosomal region, gene 1 AMMECR1 87100_at Abhydrolase domain containing 2 ABHD2 200707_at protein kinase C substrate 80K-H PRKCSH 1555594_a_at muscleblind-like (Drosophila) MBNL1 212291_at homeodomain interacting protein kinase 1 HIPK1 206748_s_at sperm associated antigen 9 SPAG9 209754_s_at thymopoietin TMPO 240277_at Solute carrier family 30 (zinc transporter), member 7 SLC30A7 1562966_at KIAA1217 KIAA1217 1553725_s_at zinc finger protein 644 ZNF644 213229_at Dicer1, Dcr-1 homolog (Drosophila) DICER1 213956_at centrosome-associated protein 350 CAP350 238461_at eukaryotic translation initiation factor 4E member 3 EIF4E3 1558093_s_at matrin 3 MATR3 212196_at Interleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 203676_at glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) GNS 204312_x_at cAMP responsive element binding protein 1 CREB1 203726_s_at laminin, alpha 3 LAMA3 238699_s_at calcium/calmodulin-dependent serine protein kinase (MAGUK family) CASK 203418_at cyclin A2 CCNA2 1563687_a_at KIAA0826 KIAA0826 1555137_a_at FYVE, RhoGEF and PH domain containing 6 FGD6 214843_s_at ubiquitin specific protease 33 USP33 213872_at Chromosome 6 open reading frame 62 C6orf62 220651_s_at MCM10 minichromosome maintenance deficient 10 (S. cerevisiae) MCM10 212016_s_at polypyrimidine tract binding protein 1 PTBP1 214154_s_at plakophilin 2 PKP2 216971_s_at plectin 1, intermediate filament binding protein 500kDa PLEC1 1554508_at phosphoinositide-3-kinase adaptor protein 1 PIK3AP1 211272_s_at diacylglycerol kinase, alpha 80kDa DGKA splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate 201742_x_at splicing factor) SFRS1 227062_at trophoblast-derived noncoding RNA TncRNA 227194_at family with sequence similarity 3, member B FAM3B 217383_at Phosphoglycerate kinase 1 PGK1 224311_s_at calcium binding protein 39 CAB39 229440_at RNA-binding protein FLJ20273 200778_s_at septin 2 SEPT2 208055_s_at hect domain and RLD 4 HERC4 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, 209970_x_at convertase) CASP1 stearoyl-CoA desaturase (delta-9-desaturase) /// stearoyl-CoA 211708_s_at desaturase (delta-9-desaturase) SCD phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole 217445_s_at synthetase GART 223686_at thiamin pyrophosphokinase 1 TPK1 228610_at SM-11044 binding protein SMBP 206061_s_at Dicer1, Dcr-1 homolog (Drosophila) DICER1 211559_s_at cyclin G2 CCNG2 1554397_s_at ubiquitin-conjugating enzyme E2-like UEV3 204058_at Malic enzyme 1, NADP(+)-dependent, cytosolic ME1 241869_at apolipoprotein L, 6 APOL6 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, 211366_x_at convertase) CASP1 216804_s_at PDZ and LIM domain 5 PDLIM5 204128_s_at replication factor C (activator 1) 3, 38kDa RFC3 1555829_at family with sequence similarity 62 (C2 domain containing) member B FAM62B 1554241_at coagulation factor C homolog, cochlin (Limulus polyphemus) COCH 209653_at karyopherin alpha 4 (importin alpha 3) KPNA4 212008_at UBX domain containing 2 UBXD2 238421_at Membrane associated DNA binding protein MNAB 203967_at CDC6 cell division cycle 6 homolog (S. cerevisiae) CDC6 221638_s_at syntaxin 16 STX16 218498_s_at ERO1-like (S. cerevisiae) ERO1L 212107_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 9 DHX9 217591_at SKI-like SKIL 201942_s_at carboxypeptidase D CPD 1555106_a_at hypothetical protein HSPC129 HSPC129 1552660_a_at hypothetical protein FLJ11193 FLJ11193 202017_at epoxide 1, microsomal (xenobiotic) EPHX1 200935_at calreticulin CALR 206788_s_at core-binding factor, beta subunit CBFB PRP4 pre-mRNA processing factor 4 homolog B (yeast) /// PRP4 pre- 211090_s_at mRNA processing factor 4 homolog B (yeast) PRPF4B 210892_s_at general transcription factor II, i GTF2I 243862_at RAS and EF hand domain containing RASEF 207456_at hepatocyte nuclear factor 4, gamma HNF4G serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 206034_at 8 SERPINB8 215509_s_at BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1 214959_s_at apoptosis inhibitor 5 API5 204059_s_at malic enzyme 1, NADP(+)-dependent, cytosolic ME1 208611_s_at spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) SPTAN1 200806_s_at heat shock 60kDa protein 1 (chaperonin) HSPD1 213048_s_at SET translocation (myeloid leukemia-associated) SET 211810_s_at galactosylceramidase (Krabbe disease) GALC 242903_at Interferon gamma receptor 1 IFNGR1 215177_s_at integrin, alpha 6 ITGA6 nuclear factor of kappa light polypeptide gene enhancer in B-cells 223217_s_at inhibitor, zeta NFKBIZ 232278_s_at DEP domain containing 1 DEPDC1 201476_s_at ribonucleotide reductase M1 polypeptide RRM1 221830_at RAP2A, member of RAS oncogene family RAP2A 212105_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 9 DHX9 223078_s_at tropomodulin 3 (ubiquitous) TMOD3 222645_s_at potassium channel tetramerisation domain containing 5 KCTD5 228030_at RNA binding motif protein 6 RBM6 205393_s_at CHK1 checkpoint homolog (S. pombe) CHEK1 1554757_a_at inositol polyphosphate-5-phosphatase, 40kDa INPP5A 225827_at eukaryotic translation initiation factor 2C, 2 EIF2C2 205729_at oncostatin M receptor OSMR 237206_at myocardin MYOCD 1569003_at transmembrane protein 49 TMEM49 1554834_a_at Ras association (RalGDS/AF-6) domain family 5 RASSF5 208721_s_at anaphase promoting complex subunit 5 ANAPC5 204881_s_at UDP-glucose ceramide glucosyltransferase UGCG 210932_s_at ring finger protein (C3H2C3 type) 6 RNF6 242277_at Phosphatase and actin regulator 2 PHACTR2 217465_at ------242844_at Protein geranylgeranyltransferase type I, beta subunit PGGT1B 243764_at V-set and immunoglobulin domain containing 1 VSIG1 217859_s_at solute carrier family 39 (zinc transporter), member 9 SLC39A9 230793_at Leucine rich repeat containing 16 LRRC16 208084_at integrin, beta 6 ITGB6 205732_s_at nuclear receptor coactivator 2 NCOA2 basic leucine zipper and W2 domains 1 /// similar to basic leucine BZW1 /// 200776_s_at zipper and W2 domains 1 LOC151579 220585_at hexokinase domain containing 1 HKDC1 203768_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS 227364_at ------protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 209895_at 1) PTPN11 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, 211368_s_at convertase) CASP1 CD74 antigen (invariant polypeptide of major histocompatibility 1567628_at complex, class II antigen-associated) CD74 205808_at aspartate beta-hydroxylase ASPH 201048_x_at RAB6A, member RAS oncogene family RAB6A 206667_s_at secretory carrier membrane protein 1 SCAMP1 223839_s_at Stearoyl-CoA desaturase (delta-9-desaturase) SCD 1558015_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 206383_s_at Ras-GTPase activating protein SH3 domain-binding protein 2 G3BP2 224173_s_at mitochondrial ribosomal protein L30 MRPL30 1552312_a_at microfibrillar-associated protein 3 MFAP3 1554273_a_at leukocyte-derived arginine aminopeptidase LRAP 220800_s_at tropomodulin 3 (ubiquitous) TMOD3 1554835_a_at UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 B3GNT5 230000_at chromosome 17 open reading frame 27 C17orf27 1555731_a_at adaptor-related protein complex 1, sigma 3 subunit AP1S3 201718_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 203767_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS 225294_s_at trafficking protein particle complex 1 TRAPPC1 TAF9-like RNA polymerase II, TATA box binding protein (TBP)- 221618_s_at associated factor, 31kDa TAF9L 231956_at KIAA1618 KIAA1618 205822_s_at 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HMGCS1 protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue 200604_s_at specific extinguisher 1) PRKAR1A 222562_s_at tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 TNKS2 230233_at RasGEF domain family, member 1B RASGEF1B 235341_at DnaJ (Hsp40) homolog, subfamily C, member 3 DNAJC3 1552478_a_at interferon regulatory factor 6 IRF6 222646_s_at ERO1-like (S. cerevisiae) ERO1L 202118_s_at copine III CPNE3 201169_s_at basic helix-loop-helix domain containing, class B, 2 BHLHB2 207223_s_at ROD1 regulator of differentiation 1 (S. pombe) ROD1 214544_s_at synaptosomal-associated protein, 23kDa SNAP23 217234_s_at villin 2 (ezrin) VIL2 209773_s_at ribonucleotide reductase M2 polypeptide RRM2 215910_s_at fibronectin type III domain containing 3A FNDC3A structural maintenance of chromosomes flexible hinge domain 1558747_at containing 1 SMCHD1 214971_s_at ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 ST6GAL1 membrane protein (CD46, trophoblast-lymphocyte cross- 211574_s_at reactive antigen) MCP 1564053_a_at YTH domain family, member 3 YTHDF3 225140_at Kruppel-like factor 3 (basic) KLF3 214040_s_at gelsolin (amyloidosis, Finnish type) GSN 203242_s_at PDZ and LIM domain 5 PDLIM5 220285_at chromosome 9 open reading frame 77 C9orf77 200769_s_at methionine adenosyltransferase II, alpha MAT2A 238673_at Transcribed locus --- 215236_s_at phosphatidylinositol binding assembly protein PICALM 214975_s_at myotubularin related protein 1 MTMR1 229982_at hypothetical protein FLJ21924 FLJ21924 201711_x_at RAN binding protein 2 RANBP2 213680_at keratin 6B KRT6B 215465_at ATP-binding cassette, sub-family A (ABC1), member 12 ABCA12 223079_s_at glutaminase GLS 209456_s_at F-box and WD-40 domain protein 11 FBXW11 238320_at trophoblast-derived noncoding RNA TncRNA 1560916_a_at dpy-19-like 1 (C. elegans) DPY19L1 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, 211367_s_at convertase) CASP1 204864_s_at interleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST AFFX- HUMISGF3A/M97 935_MB_at signal transducer and activator of transcription 1, 91kDa STAT1 208853_s_at calnexin CANX 207016_s_at aldehyde dehydrogenase 1 family, member A2 ALDH1A2 242059_at Ethanolamine kinase 1 ETNK1 1556834_at CDNA clone IMAGE:5296106, partial cds --- 1555830_s_at family with sequence similarity 62 (C2 domain containing) member B FAM62B 201251_at pyruvate kinase, muscle PKM2 209131_s_at synaptosomal-associated protein, 23kDa SNAP23 1555996_s_at eukaryotic translation initiation factor 4A, isoform 2 EIF4A2 223585_x_at kelch repeat and BTB (POZ) domain containing 2 KBTBD2 244439_at sprouty-related, EVH1 domain containing 1 SPRED1 211681_s_at PDZ and LIM domain 5 /// PDZ and LIM domain 5 PDLIM5 212514_x_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked DDX3X 243495_s_at Zinc finger protein 652 ZNF652 205018_s_at muscleblind-like 2 (Drosophila) MBNL2 229905_at Transcribed locus --- 1552619_a_at anillin, actin binding protein (scraps homolog, Drosophila) ANLN 1557910_at heat shock 90kDa protein 1, beta HSPCB UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- 220442_at acetylgalactosaminyltransferase 4 (GalNAc-T4) GALNT4 229490_s_at IQ motif containing GTPase activating protein 3 IQGAP3 201971_s_at ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A ATP6V1A 210037_s_at 2A (inducible, hepatocytes) NOS2A 200628_s_at tryptophanyl-tRNA synthetase WARS 230406_at Transcribed locus --- 1553079_at tripartite motif-containing 40 TRIM40 224221_s_at vav 3 oncogene VAV3 218273_s_at protein phosphatase 2C, magnesium-dependent, catalytic subunit PPM2C 1564164_at hypothetical protein FLJ20054 FLJ20054 206877_at MAX dimerization protein 1 MXD1 1554747_a_at septin 2 SEPT2 230352_at Phosphoribosyl pyrophosphate synthetase 2 PRPS2 1553694_a_at phosphoinositide-3-kinase, class 2, alpha polypeptide PIK3C2A 214336_s_at protein complex, subunit alpha COPA 210029_at indoleamine-pyrrole 2,3 dioxygenase INDO 210738_s_at solute carrier family 4, sodium bicarbonate cotransporter, member 4 SLC4A4 203293_s_at lectin, mannose-binding, 1 LMAN1 222385_x_at Sec61 alpha 1 subunit (S. cerevisiae) SEC61A1 1558080_s_at hypothetical protein LOC144871 LOC144871 1554339_a_at component of oligomeric golgi complex 3 COG3 216915_s_at protein tyrosine phosphatase, non-receptor type 12 PTPN12 232591_s_at transmembrane protein 30A TMEM30A 207500_at caspase 5, apoptosis-related cysteine protease CASP5 membrane cofactor protein (CD46, trophoblast-lymphocyte cross- 207549_x_at reactive antigen) MCP 201211_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked DDX3X AFFX- HUMISGF3A/M97 935_MA_at signal transducer and activator of transcription 1, 91kDa STAT1 238706_at PAP associated domain containing 4 PAPD4 224407_s_at Mst3 and SOK1-related kinase /// Mst3 and SOK1-related kinase MASK procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4- hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1564494_s_at 1) P4HB 228498_at UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B4GALT1 AFFX- HUMISGF3A/M97 935_5_at signal transducer and activator of transcription 1, 91kDa STAT1 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation 210317_s_at protein, epsilon polypeptide YWHAE 1559954_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 DDX42 207380_x_at NADPH oxidase 1 NOX1 241031_at Nuclear localized factor 1 NLF1 211016_x_at heat shock 70kDa protein 4 HSPA4 202444_s_at SPFH domain family, member 1 SPFH1 208083_s_at integrin, beta 6 ITGB6 1555326_a_at a disintegrin and metalloproteinase domain 9 (meltrin gamma) ADAM9 207356_at defensin, beta 4 DEFB4 221220_s_at SCY1-like 2 (S. cerevisiae) SCYL2 237215_s_at transferrin receptor (p90, CD71) TFRC 213548_s_at hypothetical protein H41 H41 210935_s_at WD repeat domain 1 WDR1 218748_s_at SEC10-like 1 (S. cerevisiae) SEC10L1 222932_at ets homologous factor EHF 1554878_a_at ATP-binding cassette, sub-family D (ALD), member 3 ABCD3 206917_at guanine nucleotide binding protein (G protein), alpha 13 GNA13 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 204855_at 5 SERPINB5 214007_s_at PTK9 protein tyrosine kinase 9 PTK9 230746_s_at Stanniocalcin 1 STC1 210148_at homeodomain interacting protein kinase 3 HIPK3 203294_s_at lectin, mannose-binding, 1 LMAN1 201130_s_at cadherin 1, type 1, E-cadherin (epithelial) CDH1 200796_s_at myeloid cell leukemia sequence 1 (BCL2-related) MCL1 220655_at TNFAIP3 interacting protein 3 TNIP3 1558214_s_at catenin (cadherin-associated protein), alpha 1, 102kDa CTNNA1 219795_at solute carrier family 6 (amino acid transporter), member 14 SLC6A14 205815_at regenerating islet-derived 3 alpha REG3A regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic 205886_at thread protein) REG1B regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic 209752_at thread protein) REG1A

The probe set ID originate from the Affymetrix GeneChip U133 Plus 2.0. The transcripts in red were selected for further validation with RT-PCR. The list was generated as described in Materials and Methods and identifies transcripts that are down regulated in both dysplasia and pancolitis with respect to left-sided colitis and controls.