The probe set ID originate from the Affymetrix GeneChip Human Genome U133 Plus 2.0.

(1)

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

228623_at

Transcribed locus, weakly similar to XP_517454.1 PREDICTED:

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

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

212392_s_at phosphodiesterase 4D interacting protein (myomegalin) PDE4DIP

215570_s_at hypothetical BC331191_1 /// hypothetical protein LOC284323

LOC163131 ///

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

(2)

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

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 206943_at

transforming growth factor, beta receptor I (activin A receptor type II-

like kinase, 53kDa) TGFBR1

220202_s_at membrane associated DNA binding protein MNAB

207686_s_at caspase 8, apoptosis-related cysteine protease CASP8 213087_s_at

Eukaryotic translation elongation factor 1 delta (guanine nucleotide

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

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

(3)

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

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

215931_s_at

ADP-ribosylation factor guanine nucleotide-exchange factor 2

(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

212379_at

phosphoribosylglycinamide formyltransferase,

phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole

synthetase GART

219927_at chromosome 14 open reading frame 111 C14orf111

208852_s_at calnexin CANX

212806_at KIAA0367 KIAA0367

232277_at

Solute carrier family 28 (sodium-coupled nucleoside transporter),

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 1553530_a_at

integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29

includes MDF2, MSK12) ITGB1

1553055_a_at hypothetical protein MGC19764 MGC19764

226825_s_at TPA regulated locus TPARL

212797_at sortilin 1 SORT1

(4)

205282_at

low density lipoprotein receptor-related protein 8, apolipoprotein e

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 ---

201727_s_at

ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu

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

228378_at hypothetical protein DKFZp434N2030

DKFZp434N2 030 208992_s_at

signal transducer and activator of transcription 3 (acute-phase

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

211573_x_at

transglutaminase 2 (C polypeptide, protein-glutamine-gamma-

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

(5)

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

201014_s_at

phosphoribosylaminoimidazole carboxylase,

phosphoribosylaminoimidazole succinocarboxamide synthetase PAICS

202267_at laminin, gamma 2 LAMC2

202884_s_at

protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65),

beta isoform PPP2R1B

203015_s_at synovial sarcoma, X breakpoint 2 interacting protein SSX2IP

242445_at FYVE, RhoGEF and PH domain containing 4 FGD4

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

216574_s_at

ribulose-5-phosphate-3-epimerase /// similar to Ribulose-phosphate 3- epimerase (Ribulose-5-phosphate-3-epimerase) (HUSSY-17)

RPE ///

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 200641_s_at

tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation

protein, zeta polypeptide YWHAZ

229606_at

Protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform

(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

(6)

205895_s_at nucleolar and coiled-body phosphoprotein 1 NOLC1

202886_s_at

protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65),

beta isoform PPP2R1B

232392_at Splicing factor, arginine/serine-rich 3 SFRS3

210649_s_at AT rich interactive domain 1A (SWI- like) ARID1A

203499_at EPH receptor A2 EPHA2

211762_s_at

karyopherin alpha 2 (RAG cohort 1, importin alpha 1) /// karyopherin

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

217448_s_at

chromosome 14 open reading frame 92 /// similar to Epidermal Langerhans cell protein LCP1

C14orf92 ///

LOC285412

210087_s_at myelin protein zero-like 1 MPZL1

203770_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS 221695_s_at

mitogen-activated protein kinase kinase kinase 2 /// mitogen-activated

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

214831_at

Mediator of RNA polymerase II transcription, subunit 28 homolog

(yeast) MED28

(7)

1554768_a_at MAD2 mitotic arrest deficient-like 1 (yeast) MAD2L1 216855_s_at

heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor

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

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

209853_s_at

proteasome (prosome, macropain) activator subunit 3 (PA28 gamma;

Ki) PSME3

220295_x_at DEP domain containing 1 DEPDC1

201663_s_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1

209678_s_at protein kinase C, iota PRKCI

209231_s_at dynactin 4 MGC3248

(8)

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, X chromosome 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

1554333_at DnaJ (Hsp40) homolog, subfamily A, member 4 DNAJA4 207334_s_at transforming growth factor, beta receptor II (70/80kDa) TGFBR2

241946_at zinc finger, DHHC-type containing 21 ZDHHC21

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

(9)

221194_s_at PTD016 protein LOC51136

230609_at enthoprotin ENTH

222556_at

asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate

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

212220_at proteasome (prosome, macropain) activator subunit 4 PSME4

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

221268_s_at

sphingosine-1-phosphate phosphatase 1 /// sphingosine-1-phosphate

phosphatase 1 SGPP1

201337_s_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3

213016_at Bobby sox homolog (Drosophila) BBX

202101_s_at

v-ral simian leukemia viral oncogene homolog B (ras related; GTP

binding protein) RALB

231880_at family with sequence similarity 40, member B FAM40B 211080_s_at

NIMA (never in mitosis gene a)-related kinase 2 /// NIMA (never in

mitosis gene a)-related kinase 2 NEK2

(10)

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

211547_s_at

platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit

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

200987_x_at

proteasome (prosome, macropain) activator subunit 3 (PA28 gamma;

Ki) PSME3

238761_at

Mediator of RNA polymerase II transcription, subunit 28 homolog

(yeast) MED28

211599_x_at

met proto-oncogene (hepatocyte growth factor receptor) /// met proto-

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

209896_s_at

protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome

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

1553219_a_at

Alport syndrome, mental retardation, midface hypoplasia and

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

(11)

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

201742_x_at

splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate

splicing factor) SFRS1

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

209970_x_at

caspase 1, apoptosis-related cysteine protease (interleukin 1, beta,

convertase) CASP1

211708_s_at

stearoyl-CoA desaturase (delta-9-desaturase) /// stearoyl-CoA

desaturase (delta-9-desaturase) SCD

217445_s_at

phosphoribosylglycinamide formyltransferase,

phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole

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

(12)

241869_at apolipoprotein L, 6 APOL6 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

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 hydrolase 1, microsomal (xenobiotic) EPHX1

200935_at calreticulin CALR

206788_s_at core-binding factor, beta subunit CBFB

211090_s_at

PRP4 pre-mRNA processing factor 4 homolog B (yeast) /// PRP4 pre-

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

206034_at

serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member

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

223217_s_at

nuclear factor of kappa light polypeptide gene enhancer in B-cells

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

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

(13)

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

200776_s_at

basic leucine zipper and W2 domains 1 /// similar to basic leucine zipper and W2 domains 1

BZW1 ///

LOC151579

220585_at hexokinase domain containing 1 HKDC1

203768_s_at steroid sulfatase (microsomal), arylsulfatase C, isozyme S STS

227364_at --- ---

209895_at

protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome

1) PTPN11

211368_s_at

convertase) CASP1

1567628_at

CD74 antigen (invariant polypeptide of major histocompatibility

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

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

221618_s_at

TAF9-like RNA polymerase II, TATA box binding protein (TBP)-

associated factor, 31kDa TAF9L

(14)

231956_at KIAA1618 KIAA1618 205822_s_at 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HMGCS1 200604_s_at

protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue

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

1558747_at

structural maintenance of chromosomes flexible hinge domain

containing 1 SMCHD1

214971_s_at ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 ST6GAL1 211574_s_at

membrane cofactor protein (CD46, trophoblast-lymphocyte cross-

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

200769_s_at methionine adenosyltransferase II, alpha MAT2A

238673_at Transcribed locus ---

215236_s_at phosphatidylinositol binding clathrin assembly protein PICALM

214975_s_at myotubularin related protein 1 MTMR1

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

1560916_a_at dpy-19-like 1 (C. elegans) DPY19L1

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

(15)

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

1552619_a_at anillin, actin binding protein (scraps homolog, Drosophila) ANLN

1557910_at heat shock 90kDa protein 1, beta HSPCB

220442_at

UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-

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 nitric oxide synthase 2A (inducible, hepatocytes) NOS2A

200628_s_at tryptophanyl-tRNA synthetase WARS

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

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 coatomer 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 207549_x_at

membrane cofactor protein (CD46, trophoblast-lymphocyte cross-

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

(16)

224407_s_at Mst3 and SOK1-related kinase /// Mst3 and SOK1-related kinase MASK

1564494_s_at

procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-

hydroxylase), beta polypeptide (protein disulfide isomerase-associated

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 210317_s_at

tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation

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 204855_at

serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member

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

205886_at

regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic

thread protein) REG1B

209752_at

regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic

thread protein) REG1A

The probe set ID originate from the Affymetrix GeneChip Human Genome 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

.