sign in sign up
<<
Home , ATBF1, Granzyme, MYL9, MYO1F

Table 1S. over-expressed in AILT vs. normal T-lymphocytes (corresponding to CD4+, CD8+ and HLA-DR+ elements)

Over-expression (Z Common GeneBank Description score)

9.38 232544_at AU144916 CDNA FLJ11572 fis, clone HEMBA1003373 9.179 220423_at PLA2G2D NM_012400 phospholipase A2, group IID 9.093 211719_x_at FN1 BC005858 fibronectin 1 9.005 204163_at EMILIN1 NM_007046 elastin microfibril interfacer 1 8.642 216442_x_at FN1 AK026737 fibronectin 1 8.552 220690_s_at DKFZp566O084 NM_015510 DKFZP566O084 8.204 210072_at CCL19 U88321 chemokine (CC motif) ligand 19 7.996 230047_at FLJ32810 BF439533 nab67d10.x1 Soares_NSF_F8_9W_OT_PA_P_S1 Homo sapiens cDNA clone IMAGE:3272875 3', mRNA sequence.

7.641 225575_at LIFR AI680541 leukemia inhibitory factor 7.59 215076_s_at COL3A1 AU144167 collagen, type III, alpha 1 (EhlersDanlos syndrome type IV, autosomal dominant) 7.581 204570_at COX7A1 NM_001864 cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) 7.56 217767_at C3 NM_000064 complement component 3 7.411 211981_at COL4A1 NM_001845 collagen, type IV, alpha 1 7.384 204606_at CCL21 NM_002989 chemokine (CC motif) ligand 21 7.384 201162_at IGFBP7 NM_001553 insulinlike growth factor binding protein 7 7.2 208747_s_at C1S M18767 complement component 1, s subcomponent 7.102 203915_at CXCL9 NM_002416 chemokine (CXC motif) ligand 9 6.938 222162_s_at ADAMTS1 AK023795 a disintegrinlike and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1

6.931 205890_s_at UBD NM_006398 ubiquitin D 6.813 222885_at EMCN AF205940 endomucin 6.785 201852_x_at COL3A1 AI813758 collagen, type III, alpha 1 (EhlersDanlos syndrome type IV, autosomal dominant) 6.757 212091_s_at COL6A1 AI141603 collagen, type VI, alpha 1 6.755 201744_s_at LUM NM_002345 lumican 6.712 212187_x_at PTGDS NM_000954 prostaglandin D2 synthase 21kDa (brain) 6.627 208791_at CLU M25915 clusterin (complement lysis inhibitor, SP40,40, sulfated glycoprotein 2, testosteronerepressed prostate message 2, apolipoprotein J)

6.623 208792_s_at CLU M25915 clusterin (complement lysis inhibitor, SP40,40, sulfated glycoprotein 2, testosteronerepressed prostate message 2, apolipoprotein J)

6.616 212464_s_at FN1 X02761 fibronectin 1 6.588 209183_s_at C10orf10 AL136653 10 open reading frame 10 6.515 218541_s_at C8orf4 NM_020130 chromosome 8 open reading frame 4 6.492 211161_s_at AF130082 predicted protein of HQ3121; Homo sapiens clone FLC1492 PRO3121 mRNA, complete cds.

1 6.436 226950_at T63524 yc07b04.s1 Stratagene lung (#937210) Homo sapiens cDNA clone IMAGE:79951 3', mRNA sequence. 6.373 212713_at MFAP4 R72286 microfibrillarassociated protein 4 6.286 210495_x_at FN1 AF130095 fibronectin 1 6.217 201141_at GPNMB NM_002510 glycoprotein (transmembrane) nmb 6.156 211748_x_at PTGDS BC005939 prostaglandin D2 synthase 21kDa (brain) 6.153 212077_at CALD1 AL583520 caldesmon 1 6.108 226636_at PLD1 AI378587 phospholipase D1, phophatidylcholinespecific

6.034 235229_at OR2I6 AI694413 wd83d12.x1 NCI_CGAP_Lu24 Homo sapiens cDNA clone IMAGE:2338199 3', mRNA sequence. 6.032 223395_at TARSH AB056106 target of NeshSH3 6.031 209120_at NR2F2 AL037401 subfamily 2, group F, member 2

5.997 211964_at COL4A2 X05610 collagen, type IV, alpha 2 5.966 209488_s_at RBPMS D84109 RNA binding protein with multiple splicing 5.953 225353_s_at C1QG AI184968 qe51c05.x1 Soares_fetal_lung_NbHL19W Homo sapiens cDNA clone IMAGE:1742504 3' similar to SW:C1QC_HUMAN P02747 COMPLEMENT C1Q SUBCOMPONENT, C CHAIN PRECURSOR. ;, mRNA sequence. 5.946 209395_at CHI3L1 M80927 chitinase 3like 1 (cartilage glycoprotein39) 5.946 201163_s_at IGFBP7 NM_001553 insulinlike growth factor binding protein 7 5.941 211980_at COL4A1 AI922605 collagen, type IV, alpha 1 5.883 203382_s_at APOE NM_000041 apolipoprotein E 5.883 201616_s_at CALD1 AL577531 caldesmon 1 5.881 215388_s_at HFL1 X56210 H factor (complement)like 1 5.868 217757_at A2M NM_000014 alpha2macroglobulin 5.803 204416_x_at APOC1 NM_001645 apolipoprotein CI 5.783 218232_at C1QA NM_015991 complement component 1, q subcomponent, alpha polypeptide 5.773 202052_s_at RAI14 NM_015577 retinoic acid induced 14 5.769 203381_s_at APOE N33009 apolipoprotein E 5.756 1556499_s_at COL1A1 BE221212 hu22a05.x1 NCI_CGAP_Mel15 Homo sapiens cDNA clone IMAGE:3170768 3' similar to gb:K01228 PROCOLLAGEN ALPHA 1(I) CHAIN PRECURSOR (HUMAN);, mRNA sequence. 5.741 202992_at C7 NM_000587 complement component 7 5.74 201645_at TNC NM_002160 tenascin C (hexabrachion) 5.733 200795_at SPARCL1 NM_004684 SPARClike 1 (mast9, hevin) 5.73 219825_at CYP26B1 NM_019885 cytochrome P450, family 26, subfamily B, polypeptide 1 5.725 202237_at NNMT NM_006169 nicotinamide Nmethyltransferase 5.71 209396_s_at CHI3L1 M80927 chitinase 3like 1 (cartilage glycoprotein39) 5.71 202403_s_at COL1A2 AA788711 collagen, type I, alpha 2 5.704 206134_at ADAMDEC1 NM_014479 ADAMlike, decysin 1 5.695 202112_at VWF NM_000552 von Willebrand factor 5.62 200665_s_at SPARC NM_003118 secreted protein, acidic, cysteinerich (osteonectin)

5.571 202953_at C1QB NM_000491 complement component 1, q subcomponent, beta polypeptide

2 5.557 226695_at PRRX1 AA775472 paired related 1 5.491 200986_at SERPING1 NM_000062 serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary) 5.417 203868_s_at VCAM1 NM_001078 vascular cell adhesion molecule 1 5.362 209821_at C9orf26 AB024518 chromosome 9 open reading frame 26 (NFHEV)

5.361 202404_s_at COL1A2 NM_000089 collagen, type I, alpha 2 5.347 220532_s_at LR8 NM_014020 LR8 protein 5.323 205547_s_at TAGLN NM_003186 transgelin 5.318 213428_s_at COL6A1 AA292373 collagen, type VI, alpha 1 5.291 202310_s_at COL1A1 K01228 collagen, type I, alpha 1 5.264 209496_at RARRES2 BC000069 responder (tazarotene induced) 2 5.26 1558828_s_at DKFZp586C0721 AL703532 hypothetical protein DKFZp586C0721 5.193 209121_x_at NR2F2 M64497 nuclear receptor subfamily 2, group F, member 2

5.137 217853_at TENS1 NM_022748 tensinlike SH2 domain containing 1 5.124 219134_at ELTD1 NM_022159 5.113 212067_s_at C1R AL573058 complement component 1, r subcomponent 5.044 201617_x_at CALD1 NM_004342 caldesmon 1 5.029 216598_s_at CCL2 S69738 chemokine (CC motif) ligand 2 4.982 206210_s_at CETP NM_000078 cholesteryl ester transfer protein, plasma 4.979 201058_s_at MYL9 NM_006097 , light polypeptide 9, regulatory 4.97 201655_s_at HSPG2 M85289 heparan sulfate proteoglycan 2 (perlecan) 4.948 226814_at ADAMTS9 AI431730 a disintegrinlike and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9

4.89 204533_at CXCL10 NM_001565 chemokine (CXC motif) ligand 10 4.889 202838_at FUCA1 NM_000147 fucosidase, alphaL 1, tissue 4.865 204036_at EDG2 AW269335 endothelial differentiation, lysophosphatidic acid Gproteincoupled receptor, 2 4.83 204879_at T1A2 NM_006474 lung typeI cell membraneassociated glycoprotein

4.808 226436_at RASSF4 N49935 Ras association (RalGDS/AF6) domain family 4

4.803 209074_s_at TU3A AL050264 TU3A protein 4.799 223044_at SLC40A1 AL136944 solute carrier family 40 (ironregulated transporter), member 1 4.756 203920_at NR1H3 NM_005693 nuclear receptor subfamily 1, group H, member 3

4.755 209070_s_at RGS5 AI183997 regulator of Gprotein signalling 5 4.744 201667_at GJA1 NM_000165 gap junction protein, alpha 1, 43kDa (connexin 43)

4.717 203936_s_at MMP9 NM_004994 matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)

4.613 209687_at CXCL12 U19495 chemokine (CXC motif) ligand 12 (stromal cellderived factor 1) 4.612 218345_at HCA112 NM_018487 hepatocellular carcinomaassociated antigen 112

4.571 213455_at LOC92689 W87466 hypothetical protein BC001096 4.567 201505_at LAMB1 NM_002291 laminin, beta 1 4.556 204112_s_at HNMT NM_006895 histamine Nmethyltransferase

3 4.55 208789_at PTRF BC004295 polymerase I and transcript release factor 4.504 1555724_s_at TAGLN BC010946 transgelin 4.498 226621_at FGG AI133452 fibrinogen, gamma polypeptide 4.463 208782_at FSTL1 BC000055 follistatinlike 1 4.453 201193_at IDH1 NM_005896 isocitrate dehydrogenase 1 (NADP+), soluble

4.425 224823_at MYLK AA526844 MSTP083 mRNA, complete cds 4.369 202766_s_at FBN1 NM_000138 1 (Marfan syndrome) 4.369 223235_s_at SMOC2 AB014737 SPARC related modular calcium binding 2 4.366 213553_x_at APOC1 W79394 apolipoprotein CI 4.354 212884_x_at APOE AI358867 apolipoprotein E 4.324 223820_at RBP5 AY007436 retinol binding protein 5, cellular 4.314 209071_s_at RGS5 AF159570 regulator of Gprotein signalling 5 4.292 209869_at ADRA2A AF284095 adrenergic, alpha2A, receptor 4.28 209289_at NFIB AI700518 /B 4.258 203477_at COL15A1 NM_001855 collagen, type XV, alpha 1 4.249 202252_at RAB13 NM_002870 RAB13, member RAS oncogene family 4.244 225664_at COL12A1 AA788946 collagen, type XII, alpha 1 4.235 202465_at PCOLCE NM_002593 procollagen Cendopeptidase enhancer 4.227 209210_s_at PLEKHC1 Z24725 pleckstrin homology domain containing, family C (with FERM domain) member 1 4.222 202800_at SLC1A3 NM_004172 solute carrier family 1 (glial high affinity glutamate transporter), member 3 4.212 203060_s_at PAPSS2 AF074331 Homo sapiens PAPS synthetase2 (PAPSS2) mRNA, complete cds. 4.183 202133_at TAZ BF674349 transcriptional coactivator with PDZbinding motif (TAZ) 4.151 212724_at ARHE BG054844 ras homolog gene family, member E 4.115 220301_at C18orf14 NM_024781 hypothetical protein FLJ23594 4.114 203131_at PDGFRA NM_006206 plateletderived growth factor receptor, alpha polypeptide 4.113 208335_s_at FY NM_002036 Duffy blood group 4.104 212667_at SPARC AL575922 secreted protein, acidic, cysteinerich (osteonectin)

4.091 207173_x_at CDH11 D21254 cadherin 11, type 2, OBcadherin (osteoblast)

4.085 210839_s_at ENPP2 D45421 ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin)

4.084 212192_at KCTD12 AI718937 potassium channel tetramerisation domain containing 12 4.083 226804_at FAM20A AI632223 family with sequence similarity 20, member A

4.08 232113_at N90870 MRNA; cDNA DKFZp564B182 (from clone DKFZp564B182) 4.053 225681_at CTHRC1 AA584310 collagen triple helix repeat containing 1 4.048 225897_at MARCKS AI709406 myristoylated alaninerich protein kinase C substrate 4.039 202411_at IFI27 NM_005532 interferon, alphainducible protein 27 4.015 226408_at TEAD2 AA905942 CD37 antigen 4.006 208451_s_at C4A NM_000592 complement component 4A 4.004 203979_at CYP27A1 NM_000784 cytochrome P450, family 27, subfamily A, polypeptide 1 3.984 222453_at CYBRD1 AL136693 cytochrome b reductase 1

4 3.975 210986_s_at TPM1 Z24727 1 (alpha) 3.943 202555_s_at MYLK NM_005965 myosin, light polypeptide kinase 3.935 205392_s_at CCL14 NM_004166 chemokine (CC motif) ligand 15 3.918 202202_s_at LAMA4 NM_002290 laminin, alpha 4 3.914 202238_s_at NNMT NM_006169 nicotinamide Nmethyltransferase 3.908 220005_at GPR86 NM_023914 G proteincoupled receptor 86 3.906 207714_s_at SERPINH1 NM_004353 synonyms: CBP1, CBP2, gp46, HSP47, RAA47, SERPINH2; collagenbinding protein 1; colligin1; collagenbinding protein 2; colligin2; heat shock protein 47; rheumatoid arthritis antigen A47; go_component: endoplasmic reticulum [goid 0005783] [evidence TAS] [pmid 7656593]; go_function: collagen binding [goid 0005518] [evidence NR]; go_function: inhibitor activity [goid 0004867] [evidence P] [pmid 1309665]; go_function: heat shock protein activity [goid 0003773] [evidence TAS] [pmid 1309665]; go_function: serpin [goid 0004868] [evidence IEA]; go_process: response to stress [goid 0006950] [evidence TAS] [pmid 1309665]; go_process: heat shock response [goid 0006951] [evidence P]; Homo sapiens serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) (SERPINH1), mRNA.

3.88 225040_s_at RPE AV699857 AV699857 GKC Homo sapiens cDNA clone GKCGFG07 3', mRNA sequence. 3.876 232458_at COL3A1 AU146808 collagen, type III, alpha 1 (EhlersDanlos syndrome type IV, autosomal dominant) 3.863 221210_s_at NPL NM_030769 Nacetylneuraminate pyruvate (dihydrodipicolinate synthase) 3.859 201279_s_at DAB2 BC003064 disabled homolog 2, mitogenresponsive phosphoprotein (Drosophila) 3.839 207030_s_at CSRP2 NM_001321 cysteine and glycinerich protein 2 3.838 200974_at ACTA2 NM_001613 , alpha 2, smooth muscle, aorta 3.836 227235_at AI758408 CDNA FLJ42250 fis, clone TKIDN2007828 3.834 211959_at IGFBP5 AW007532 ws52h07.x1 NCI_CGAP_Brn25 Homo sapiens cDNA clone IMAGE:2500861 3', mRNA sequence. 3.831 221958_s_at FLJ23091 AA775681 putative NFkB activating protein 373 3.823 1552798_a_at TLR4 NM_138557 tolllike receptor 4 3.805 213869_x_at THY1 AA218868 zr01g01.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone IMAGE:650256 3', mRNA sequence. 3.783 206295_at IL18 NM_001562 interleukin 18 (interferongammainducing factor)

3.78 203324_s_at CAV2 NM_001233 caveolin 2 3.766 211651_s_at LAMB1 M20206 laminin, beta 1 3.763 228176_at EDG3 AA534817 endothelial differentiation, sphingolipid Gproteincoupled receptor, 3 3.74 221748_s_at TNS AL046979 tensin 3.729 203817_at GUCY1B3 W93728 guanylate cyclase 1, soluble, beta 3 5 3.724 217890_s_at PARVA NM_018222 parvin, alpha 3.71 212698_s_at SEPT10 BF966021 septin 10 3.703 238332_at ANKRD29 AI307802 hypothetical protein LOC147463 3.693 201280_s_at DAB2 NM_001343 disabled homolog 2, mitogenresponsive phosphoprotein (Drosophila) 3.68 210139_s_at PMP22 L03203 peripheral myelin protein 22 3.676 202436_s_at CYP1B1 AU144855 cytochrome P450, family 1, subfamily B, polypeptide 1 3.658 224894_at YAP1 BF247906 Yesassociated protein 1, 65kDa 3.625 203570_at LOXL1 NM_005576 lysyl oxidaselike 1 3.613 219918_s_at ASPM NM_018123 synonyms: MCPH5, FLJ10517, FLJ10549; microcephaly, primary autosomal recessive 5; Homo sapiens asp (abnormal spindle)like, microcephaly associated (Drosophila) (ASPM), mRNA. 3.61 224694_at ANTXR1 AF279145 anthrax toxin receptor 1 3.584 203473_at SLCO2B1 NM_007256 solute carrier organic anion transporter family, member 2B1 3.579 212226_s_at PPAP2B AA628586 phosphatidic acid phosphatase type 2B 3.561 211966_at COL4A2 AA909035 collagen, type IV, alpha 2 3.556 228581_at KCNJ10 AW071744 potassium inwardlyrectifying channel, subfamily J, member 10 3.555 225868_at TRIM47 AW249467 tripartite motifcontaining 47 3.545 203454_s_at ATOX1 NM_004045 ATX1 antioxidant protein 1 homolog (yeast) 3.543 202017_at EPHX1 NM_000120 epoxide 1, microsomal (xenobiotic)

3.541 212647_at RRAS NM_006270 related RAS viral (rras) oncogene homolog 3.524 204677_at CDH5 NM_001795 cadherin 5, type 2, VEcadherin (vascular epithelium) 3.519 205943_at TDO2 NM_005651 tryptophan 2,3dioxygenase 3.516 226837_at SPRED1 BE967019 sproutyrelated, EVH1 domain containing 1 3.511 227297_at ITGA9 AI479176 integrin, alpha 9 3.51 228772_at HNMT AU157303 histamine Nmethyltransferase 3.471 228220_at LOC115548 AI627666 hypothetical protein BC014311 3.451 214880_x_at CALD1 D90453 caldesmon 1 3.449 208851_s_at THY1 AL161958 Thy1 cell surface antigen 3.434 225442_at DDR2 AI799915 discoidin domain receptor family, member 2 3.431 223204_at DKFZp434L142 AF260333 hypothetical protein DKFZp434L142 3.428 202920_at ANK2 BF726212 2, neuronal 3.426 209568_s_at RGL1 AF186779 ral guanine nucleotide dissociation stimulatorlike 1

3.392 229218_at COL1A2 AA628535 collagen, type I, alpha 2 3.384 229121_at BE857553 CDNA FLJ44441 fis, clone UTERU2020242 3.374 210757_x_at DAB2 AF188298 disabled homolog 2, mitogenresponsive phosphoprotein (Drosophila) 3.37 202357_s_at BF NM_001710 Bfactor, properdin 3.369 203910_at PARG1 NM_004815 PTPL1associated RhoGAP 1 3.353 225646_at CTSC AI246687 C 3.35 229800_at AI129626 CDNA FLJ41433 fis, clone BRHIP2007307 3.349 203632_s_at GPRC5B NM_016235 G proteincoupled receptor, family C, group 5, member B 3.34 209487_at RBPMS D84109 RNA binding protein with multiple splicing 3.311 221246_x_at TNS NM_018274 3.285 225242_s_at URB AW303375 steroid sensitive gene 1

6 3.283 203058_s_at PAPSS2 AW299958 3'phosphoadenosine 5'phosphosulfate synthase 2

3.276 202087_s_at CTSL NM_001912 cathepsin L 3.267 221900_at COL8A2 AI806793 collagen, type VIII, alpha 2 3.249 200663_at CD63 NM_001780 CD63 antigen (melanoma 1 antigen) 3.245 208161_s_at ABCC3 NM_020037 ATPbinding cassette, subfamily C (CFTR/MRP), member 3 3.214 228776_at AA430014 Transcribed sequence with moderate similarity to protein ref:NP_055301.1 (H.sapiens) neuronal thread protein [Homo sapiens]

3.212 212354_at SULF1 BE500977 sulfatase 1 3.21 240440_at NPL AI368358 Nacetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 3.204 213817_at AL049435 MRNA; cDNA DKFZp586B0220 (from clone DKFZp586B0220) 3.18 226000_at DKFZp547A023 AI423056 hypothetical protein DKFZp547A023 3.18 202011_at TJP1 NM_003257 tight junction protein 1 (zona occludens 1) 3.164 228143_at CP AI684991 ceruloplasmin (ferroxidase) 3.148 219385_at SLAMF8 NM_020125 SLAM family member 8 3.142 233461_x_at ZNF226 AK023091 protein 226 3.138 225308_s_at KIAA1728 AB051515 KIAA1728 protein 3.13 229802_at WISP1 AA147884 WNT1 inducible signaling pathway protein 1 3.103 212606_at WDFY3 AL536319 AL536319 Homo sapiens FETAL BRAIN Homo sapiens cDNA clone CS0DF015YG13 3PRIME, mRNA sequence.

3.1 204359_at FLRT2 NM_013231 fibronectin leucine rich transmembrane protein 2

3.093 221584_s_at KCNMA1 U11058 potassium large conductance calciumactivated channel, subfamily M, alpha member 1

3.076 223503_at DKFZP566N034 AF255647 hypothetical protein DKFZp566N034 3.066 230291_s_at NFIB T90642 nuclear factor I/B 3.019 239577_at AV699781 AV699781 GKC Homo sapiens cDNA clone GKCEKC01 3', mRNA sequence. 3.005 207836_s_at RBPMS NM_006867 RNA binding protein with multiple splicing 2.982 202878_s_at C1QR1 NM_012072 complement component 1, q subcomponent, receptor 1 2.968 204517_at PPIC BE962749 601656143R1 NIH_MGC_66 Homo sapiens cDNA clone IMAGE:3855754 3', mRNA sequence. 2.961 235571_at AW300953 xk10b12.x1 NCI_CGAP_Co20 Homo sapiens cDNA clone IMAGE:2666303 3', mRNA sequence. 2.946 210163_at CXCL11 AF030514 chemokine (CXC motif) ligand 11 2.918 208923_at CYFIP1 BC005097 cytoplasmic FMR1 interacting protein 1 2.912 201431_s_at DPYSL3 NM_001387 dihydropyrimidinaselike 3 2.866 200771_at LAMC1 NM_002293 laminin, gamma 1 (formerly LAMB2) 2.859 240481_at BE502509 Transcribed sequences 2.853 212950_at GPR116 BF941499 G proteincoupled receptor 116 2.846 209652_s_at PGF BC001422 placental growth factor, vascular endothelial growth factorrelated protein 2.834 218231_at NAGK NM_017567 Nacetylglucosamine kinase

7 2.817 221898_at T1A2 AU154455 AU154455 NT2RP4 Homo sapiens cDNA clone NT2RP4001145 3', mRNA sequence. 2.771 1554018_at GPNMB BC011595 glycoprotein (transmembrane) nmb 2.719 226103_at NEXN AF114264 nexilin (F actin binding protein) 2.706 209596_at DKFZp564I1922 AF245505 adlican 2.695 201809_s_at ENG NM_000118 endoglin (OslerRenduWeber syndrome 1) 2.694 228186_s_at THSD2 BF589322 thrombospondin, type I, domain 2 2.674 221667_s_at HSPB8 AF133207 heat shock 27kDa protein 8 2.613 226834_at ASAM BG112263 adipocytespecific adhesion molecule 2.613 212412_at LIM AV715767 LIM protein (similar to rat protein kinase Cbinding enigma) 2.563 205003_at DOCK4 NM_014705 dedicator of cytokinesis 4 2.546 227792_at AA490685 CDNA: FLJ22994 fis, clone KAT11918 2.525 226603_at FLJ39885 BE966604 601660289R1 NIH_MGC_71 Homo sapiens cDNA clone IMAGE:3905950 3', mRNA sequence. 2.512 216620_s_at ARHGEF10 AF009205 Rho guanine nucleotide exchange factor (GEF) 10

2.472 204037_at EDG2 BF055366 endothelial differentiation, lysophosphatidic acid Gproteincoupled receptor, 2 2.467 209785_s_at PLA2G4C AF065214 phospholipase A2, group IVC (cytosolic, calciumindependent) 2.46 202976_s_at RHOBTB3 NM_014899 Rhorelated BTB domain containing 3 2.458 203052_at C2 NM_000063 complement component 2 2.397 225202_at RHOBTB3 BE620739 Rhorelated BTB domain containing 3 2.33 1552626_a_at DKFZP566N034 NM_030923 hypothetical protein DKFZp566N034

8 Table 2S. Genes down-regulated in AILT vs. normal T-lymphocytes (corresponding to CD4+, CD8+ and HLA-DR+ elements)

Down-regulation Gene Common GeneBank Description (Z score) 10.754 1556873_at RKHD2 BC032952 Homo sapiens hypothetical protein LOC51320, mRNA (cDNA clone IMAGE:4828930), partial cds. 9.409 242832_at PER1 AI743776 period homolog 1 (Drosophila) 7.904 205239_at AREG NM_001657 amphiregulin (schwannoma-derived growth factor) 7.348 230380_at DKFZP564I0422 AW235671 hypothetical protein DKFZp564I0422 7.322 225557_at AXUD1 AI091372 AXIN1 up-regulated 1 7.219 37028_at PPP1R15A U83981 protein phosphatase 1, regulatory (inhibitor) subunit 15A 7.182 206877_at MAD NM_002357 MAX dimerization protein 1 7.154 230511_at CREM AI800640 cAMP responsive element modulator 6.929 202768_at FOSB NM_006732 FBJ murine osteosarcoma viral oncogene homolog B 6.872 225951_s_at CHD2 AV756026 chromodomain helicase DNA binding protein 2 6.75 212225_at SUI1 AL516854 putative translation initiation factor 6.721 220046_s_at CCNL1 NM_020307 cyclin L1 6.65 204622_x_at NR4A2 NM_006186 nuclear receptor subfamily 4, group A, member 2 6.564 204621_s_at NR4A2 AI935096 nuclear receptor subfamily 4, group A, member 2 6.554 216248_s_at NR4A2 S77154 nuclear receptor subfamily 4, group A, member 2 6.42 202014_at PPP1R15A NM_014330 protein phosphatase 1, regulatory (inhibitor) subunit 15A 6.361 227558_at CBX4 AI570531 chromobox homolog 4 (Pc class homolog, Drosophila) 6.348 219228_at ZNF331 NM_018555 zinc finger protein 331 6.341 230233_at RASGEF1B BF110534 RasGEF domain family, member 1B 6.253 242904_x_at MGC8721 AI351653 qr06h10.x1 Soares_total_fetus_Nb2HF8_9w Homo sapiens cDNA clone IMAGE:1940131 3' similar to contains MER22.t1 TAR1 repetitive element ;, mRNA sequence. 6.036 217741_s_at ZNF216 AW471220 zinc finger protein 216 5.991 209959_at NR4A3 U12767 Human mitogen induced nuclear orphan receptor (MINOR) mRNA, complete cds. 5.973 1555832_s_at BU683415 MRNA; cDNA DKFZp564C2063 (from clone DKFZp564C2063) 5.961 204286_s_at PMAIP1 NM_021127 phorbol-12-myristate-13-acetate-induced protein 1 5.929 222408_s_at CGI-127 BC000836 yippee protein 5.914 209967_s_at CREM D14826 5.703 1559975_at BTG1 BC009050 Hypothetical protein LOC256021 (LOC256021), mRNA 5.688 218723_s_at RGC32 NM_014059 response gene to complement 32 5.677 204285_s_at PMAIP1 AI857639 phorbol-12-myristate-13-acetate-induced protein 1

9 5.582 214508_x_at CREM U44836 cAMP responsive element modulator 5.58 224606_at BG250721 602363024F1 NIH_MGC_90 Homo sapiens cDNA clone IMAGE:4471541 5', mRNA sequence. 5.519 211999_at H3F3B Z48950 H.sapiens hH3.3B gene for histone H3.3. 5.513 207630_s_at CREM NM_001881 cAMP responsive element modulator 5.505 207978_s_at NR4A3 NM_006981 nuclear receptor subfamily 4, group A, member 3 5.43 227613_at AW450874 Full length insert cDNA clone YZ93G08 5.411 201464_x_at JUN BG491844 v-jun sarcoma 17 oncogene homolog (avian) 5.402 231182_at WASPIP BF446719 Wiskott-Aldrich syndrome protein interacting protein 5.307 217783_s_at CGI-127 NM_016061 yippee protein 5.267 222044_at C20orf67 AI199589 open reading frame 67 5.241 210837_s_at PDE4D AF012074 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) 5.096 214290_s_at HIST2H2AA AI313324 ta77f02.x2 NCI_CGAP_HSC2 Homo sapiens cDNA clone IMAGE:2050107 3' similar to gb:L19779 HISTONE H2A.1 (HUMAN);, mRNA sequence. 5.091 212130_x_at SUI1 AL537707 putative translation initiation factor 5.054 238633_at EPC1 W93523 enhancer of polycomb homolog 1 (Drosophila) 5.051 208078_s_at TCF8 NM_030751 8 (represses interleukin 2 expression) 5.019 208961_s_at COPEB AB017493 core promoter element binding protein 4.97 224569_s_at IRF2BP2 AW242432 interferon regulatory factor 2 binding protein 2 4.956 208706_s_at EIF5 AK026933 eukaryotic translation initiation factor 5 4.926 221841_s_at BF514079 Kruppel-like factor 4 (gut) 4.874 213538_at SON AI936458 SON DNA binding protein 4.851 218611_at IER5 NM_016545 immediate early response 5 4.851 212227_x_at SUI1 W67644 putative translation initiation factor 4.846 209510_at RNF139 AF064801 ring finger 139 4.836 202643_s_at TNFAIP3 AI738896 tumor necrosis factor, alpha-induced protein 3 4.793 202021_x_at SUI1 AF083441 putative translation initiation factor 4.768 209795_at CD69 L07555 CD69 antigen (p60, early T-cell activation antigen) 4.731 222669_s_at SBDS AK001779 Shwachman-Bodian-Diamond syndrome 4.728 202146_at IFRD1 AA747426 interferon-related developmental regulator 1 4.727 208960_s_at COPEB BE675435 core promoter element binding protein 4.668 202497_x_at SLC2A3 AI631159 solute carrier family 2 (facilitated glucose transporter), member 3 4.652 228098_s_at MYLIP AW292746 myosin regulatory light chain interacting protein 4.642 238389_s_at AI458208 Transcribed sequences 4.64 202388_at RGS2 NM_002923 regulator of G-protein signalling 2, 24kDa 4.637 1568665_at RNF103 BC022477 ring finger protein 103 4.633 219312_s_at ZBTB10 NM_023929 zinc finger and BTB domain containing 10

10 4.613 226153_s_at CNOT6L AW514857 CCR4-NOT transcription complex, subunit 6-like 4.605 228562_at ZBTB10 N29918 zinc finger and BTB domain containing 10 4.602 200731_s_at PTP4A1 AW165960 protein tyrosine phosphatase type IVA, member 1 4.565 221563_at DUSP10 N36770 dual specificity phosphatase 10 4.547 200733_s_at PTP4A1 U48296 protein tyrosine phosphatase type IVA, member 1 4.535 216834_at RGS1 S59049 regulator of G-protein signalling 1 4.503 201566_x_at ID2 D13891 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein 4.473 228812_at AI652899 Transcribed sequence with weak similarity to protein ref:NP_060265.1 (H.sapiens) hypothetical protein FLJ20378 [Homo sapiens] 4.453 211458_s_at GABARAPL1 AF180519 GABA(A) receptors associated protein like 3 4.444 216027_at DJ971N18.2 AI005473 hypothetical protein DJ971N18.2 4.437 218280_x_at HIST2H2AA NM_003516 histone 2, H2aa 4.437 204141_at TUBB NM_001069 , beta polypeptide 4.436 202704_at TOB1 AA675892 transducer of ERBB2, 1 4.417 235739_at AA523939 Transcribed sequences 4.406 216236_s_at SLC2A14 AL110298 solute carrier family 2 (facilitated glucose transporter), member 14 4.395 203752_s_at JUND NM_005354 jun D proto-oncogene 4.389 228097_at MYLIP AW292746 myosin regulatory light chain interacting protein 4.368 204794_at DUSP2 NM_004418 dual specificity phosphatase 2 4.365 207574_s_at GADD45B NM_015675 growth arrest and DNA-damage- inducible, beta 4.362 205596_s_at SMURF2 AY014180 E3 ubiquitin SMURF2 4.357 218319_at PELI1 NM_020651 pellino homolog 1 (Drosophila) 4.355 225199_at PRO0149 AA526970 ni06c09.s1 NCI_CGAP_Br2 Homo sapiens cDNA clone IMAGE:967216 3', mRNA sequence. 4.353 212665_at TIPARP AL556438 TCDD-inducible poly(ADP-ribose) polymerase 4.342 235102_x_at AI684439 Transcribed sequences 4.341 202988_s_at RGS1 NM_002922 regulator of G-protein signalling 1 4.318 211998_at H3F3B AW138159 H3 histone, family 3B (H3.3B) 4.282 241985_at JMY AI814405 junction-mediating and regulatory protein 4.281 1556874_a_at RKHD2 BC032952 Homo sapiens hypothetical protein LOC51320, mRNA (cDNA clone IMAGE:4828930), partial cds. 4.253 201565_s_at ID2 NM_002166 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein 4.239 212508_at MOAP1 AK024029 modulator of 1 4.225 204897_at PTGER4 AA897516 prostaglandin E receptor 4 (subtype EP4) 4.223 1554036_at ZBTB24 BC036731 zinc finger protein 450 4.201 221763_at JMJD1C AI694023 thyroid interactor 8 4.17 202147_s_at IFRD1 NM_001550 interferon-related developmental regulator 1

11 4.15 217672_x_at SUI1 BF114906 Transcribed sequence with weak similarity to protein pir:A43932 (H.sapiens) A43932 mucin 2 precursor, intestinal - human 4.139 208763_s_at DSIPI AL110191 delta sleep inducing peptide, immunoreactor 4.125 209185_s_at IRS2 AF073310 insulin receptor substrate 2 4.125 41387_r_at JMJD3 AB002344 jumonji domain containing 3 4.114 230048_at BF061555 Transcribed sequence with moderate similarity to protein pdb:1LBG (E. coli) B Chain B, Lactose Operon Repressor Bound To 21- Symmetric Operator Dna, Alpha Carbons Only 4.093 226034_at BE222344 Clone IMAGE:3881549, mRNA 4.086 223310_x_at IPLA2(GAMMA) AF217519 intracellular membrane-associated calcium-independent phospholipase A2 gamma 4.082 223130_s_at MYLIP AF212221 myosin regulatory light chain interacting protein 4.069 218012_at SE20-4 NM_022117 cutaneous T-cell lymphoma-associated tumor antigen se20-4 4.062 1557257_at BCL10 AA994334 B-cell CLL/lymphoma 10 4.062 200730_s_at PTP4A1 BF576710 602135085F1 NIH_MGC_81 Homo sapiens cDNA clone IMAGE:4290141 5', mRNA sequence. 4.046 227521_at FBXO33 N22902 yx66e03.s1 Soares melanocyte 2NbHM Homo sapiens cDNA clone IMAGE:266716 3', mRNA sequence. 4.014 200920_s_at BTG1 AL535380 B-cell translocation gene 1, anti- proliferative 4.011 202644_s_at TNFAIP3 NM_006290 tumor necrosis factor, alpha-induced protein 3 4.008 211840_s_at PDE4D U50157 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) 3.99 205214_at STK17B NM_004226 serine/threonine kinase 17b (apoptosis- inducing) 3.973 1555411_a_at CCNL1 AF367476 cyclin L1 3.972 222870_s_at B3GNT1 AF288208 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 1 3.961 201531_at ZFP36 NM_003407 zinc finger protein 36, C3H type, homolog (mouse) 3.905 226352_at JMY BF447037 junction-mediating and regulatory protein 3.904 230820_at SMURF2 BF111169 E3 ubiquitin ligase SMURF2 3.891 212689_s_at JMJD1A AA524505 jumonji domain containing 1 3.888 89948_at C20orf67 AI743331 chromosome 20 open reading frame 67 3.856 210054_at C4orf15 BC003648 hypothetical protein MGC4701 3.787 217739_s_at PBEF1 NM_005746 pre-B-cell colony enhancing factor 1 3.778 203725_at GADD45A NM_001924 growth arrest and DNA-damage- inducible, alpha 3.769 202499_s_at SLC2A3 NM_006931 solute carrier family 2 (facilitated glucose transporter), member 3

12 3.75 222309_at AW972292 Transcribed sequence with strong similarity to protein sp:P39194 (H.sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 3.743 204258_at CHD1 NM_001270 chromodomain helicase DNA binding protein 1 3.729 1569136_at MGAT4A BC031487 mannosyl (alpha-1,3-)-glycoprotein beta- 1,4-N-acetylglucosaminyltransferase, isoenzyme A 3.726 208810_at DNAJB6 AF080569 DnaJ (Hsp40) homolog, subfamily B, member 6 3.706 238893_at LOC338758 AI377324 Hypothetical protein LOC338758, mRNA (cDNA clone IMAGE:5299152), partial cds 3.694 228702_at FLJ43663 AL569506 hypothetical protein FLJ43663 3.689 231863_at ING3 AF161419 inhibitor of growth family, member 3 3.68 212293_at HIPK1 BG111260 homeodomain interacting protein kinase 1 3.648 214683_s_at CLK1 AI251890 CDC-like kinase 1 3.645 202302_s_at FLJ11021 NM_023012 similar to splicing factor, arginine/serine-rich 4 3.608 223982_s_at IPLA2(GAMMA) AB041261 intracellular membrane-associated calcium-independent phospholipase A2 gamma 3.605 244677_at PER1 AA416756 period homolog 1 (Drosophila) 3.602 210396_s_at LAT1-3TM AF271775 Similar to My016 protein (LOC339088), mRNA 3.587 230156_x_at CHD2 AI933049 chromodomain helicase DNA binding protein 2 3.581 236213_at AI809760 Transcribed sequence with strong similarity to protein ref:NP_060117.2 (H.sapiens) FtsJ homolog 3 3.579 205027_s_at MAP3K8 NM_005204 mitogen-activated protein kinase kinase kinase 8 3.577 1568627_at KIAA1387 BC032531 KIAA1387 protein 3.559 224838_at FOXP1 AK026898 forkhead box P1 3.557 225262_at FOSL2 AI670862 FOS-like antigen 2 3.554 238623_at MAP3K4 AI633559 mitogen-activated protein kinase kinase kinase 4 3.539 227044_at AV705507 Transcribed sequences 3.529 1554037_a_at ZBTB24 BC036731 zinc finger protein 450 3.498 1554929_at KIAA0999 BC035583 KIAA0999 protein 3.491 224836_at C20orf110 AL109824 3.457 218936_s_at HSPC128 NM_014167 HSPC128 protein 3.452 222088_s_at SLC2A14 AA778684 solute carrier family 2 (facilitated glucose transporter), member 14 3.441 239438_at RAPGEF6 AW169970 Rap guanine nucleotide exchange factor (GEF) 6 3.424 226650_at LOC90637 AI984061 hypothetical protein LOC90637 3.423 209184_s_at IRS2 BF700086 602127569F1 NIH_MGC_56 Homo sapiens cDNA clone IMAGE:4284401 5', mRNA sequence. 3.412 223287_s_at FOXP1 AF146696 forkhead box P1 3.412 224692_at PPP1R15B BF796046 protein phosphatase 1, regulatory (inhibitor) subunit 15B

13 3.412 203380_x_at SFRS5 NM_006925 splicing factor, arginine/serine-rich 5 3.395 200921_s_at BTG1 NM_001731 B-cell translocation gene 1, anti- proliferative 3.394 238228_at COG3 AI732206 component of oligomeric golgi complex 3 3.388 210836_x_at PDE4D AF012073 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) 3.386 201465_s_at JUN BC002646 v-jun sarcoma virus 17 oncogene homolog (avian) 3.366 200892_s_at SFRS10 BC000451 splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) 3.353 227747_at LOC196264 AA772172 hypothetical protein LOC196264 3.306 213958_at CD6 AW134823 CD6 antigen 3.293 202393_s_at TIEG NM_005655 TGFB inducible early growth response 3.292 241027_at OPA1 BE858373 optic atrophy 1 (autosomal dominant) 3.269 200732_s_at PTP4A1 AL578310 protein tyrosine phosphatase type IVA, member 1 3.264 212493_s_at HYPB AI761110 huntingtin interacting protein B 3.255 1554661_s_at FLJ32001 BC036200 hypothetical protein FLJ32001 3.254 1553736_at MGC23401 NM_144982 hypothetical protein MGC23401 3.253 202861_at PER1 NM_002616 period homolog 1 (Drosophila) 3.229 228967_at SUI1 BE964053 putative translation initiation factor 3.205 237510_at MYNN AI939472 myoneurin 3.197 220319_s_at MYLIP NM_013262 myosin regulatory light chain interacting protein 3.193 201210_at DDX3X NM_001356 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 3.169 209604_s_at GATA3 BC003070 GATA binding protein 3 3.164 210275_s_at ZNF216 AF062347 zinc finger protein 216 3.145 218603_at HECA NM_016217 headcase homolog (Drosophila) 3.132 200847_s_at MGC8721 NM_016127 hypothetical protein MGC8721 3.132 1554089_s_at SBDS BC010183 Shwachman-Bodian-Diamond syndrome pseudogene 3.131 40446_at PHF1 AL021366 3.128 210666_at IDS AF050145 iduronate 2-sulfatase (Hunter syndrome) 3.125 229844_at AI699465 Transcribed sequences 3.101 217682_at PRO0149 AW503390 PRO0149 protein 3.094 226970_at FBXO33 AI690694 F-box only protein 33 3.062 228193_s_at RGC32 AI744499 response gene to complement 32 3.056 220086_at ZNFN1A5 NM_022466 zinc finger protein, subfamily 1A, 5 3.02 1556239_a_at BC040322 Clone IMAGE:4828492, mRNA 2.993 231124_x_at LY9 AI524095 lymphocyte antigen 9 2.991 223129_x_at MYLIP T63512 myosin regulatory light chain interacting protein 2.986 206035_at REL NM_002908 v- reticuloendotheliosis viral oncogene homolog (avian) 2.983 224454_at EKI1 BC006111 ethanolamine kinase 2.973 239334_at AI349167 Transcribed sequences 2.951 208924_at RNF11 AB024703 ring finger protein 11 2.947 1554719_at NDUFA10 BC031332 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa

14 2.946 200797_s_at MCL1 AI275690 qw03a03.x1 NCI_CGAP_Ut3 Homo sapiens cDNA clone IMAGE:1989964 3', mRNA sequence. 2.931 205281_s_at PIGA NM_002641 phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria) 2.901 240369_at TTC7 AW195569 tetratricopeptide repeat domain 7 2.873 36829_at PER1 AF022991 period homolog 1 (Drosophila) 2.849 224610_at RNU22 AL530869 AL530869 Homo sapiens NEUROBLASTOMA COT 50- NORMALIZED Homo sapiens cDNA clone CS0DD008YK05 3-PRIME, mRNA sequence. 2.838 218871_x_at GALNACT-2 NM_018590 chondroitin sulfate GalNAcT-2 2.805 228181_at SLC30A1 AI553933 solute carrier family 30 (zinc transporter), member 1 2.8 239494_at BF336159 Clone IMAGE:4860747, mRNA 2.796 201300_s_at PRNP NM_000311 prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia) 2.75 226830_x_at CHD2 BG339245 chromodomain helicase DNA binding protein 2 2.735 1568768_s_at BRE AW080339 ribokinase 2.686 210954_s_at KIAA0669 AF201292 KIAA0669 gene product 2.671 1554309_at EIF4G3 BC030578 eukaryotic translation initiation factor 4 gamma, 3 2.669 237718_at EIF4E AA913840 eukaryotic translation initiation factor 4E 2.656 201197_at AMD1 NM_001634 adenosylmethionine decarboxylase 1 2.625 203429_s_at C1orf9 NM_016227 chromosome 1 open reading frame 9 2.545 208840_s_at G3BP2 AU149503 Ras-GTPase activating protein SH3 domain-binding protein 2 2.266 222045_s_at C20orf67 AI199589 chromosome 20 open reading frame 67 2.205 208615_s_at PTP4A2 BF795101 protein tyrosine phosphatase type IVA, member 2

15 Table 3S. Top 10 categories of genes differentially expressed in AILT vs. normal T-lymphocytes (corresponding to CD4+, CD8+ and HLA-DR+ elements), ranked according with analysis performed with EASE

System Gene Category List List Population Population Fisher exact test Affymetrix probesets Hits Total Hits Total probability

GO Biological complement 12 272 41 12602 6.63e-010 200986_AT; 202357_ Process activation 203052_AT; 208451_ 208792_S_AT; 21206 225353_S_AT

GO Biological complement 10 272 31 12602 1.15e-008 200986_AT; 202953_ Process activation\, classical 208747_S_AT; 20879 pathway 212067_S_AT; 21776 GO Biological humoral defense 16 272 128 12602 9.93e-008 200986_AT; 202357_ Process mechanism (sensu 203052_AT; 204517_ Vertebrata) 205890_S_AT; 20845 208791_AT; 208792_ 216248_S_AT; 21776 231124_X_AT GO Biological humoral immune 18 272 170 12602 1.46e-007 200986_AT; 202357_ Process response 203052_AT; 204517_ 205890_S_AT; 20629 208747_S_AT; 20879 212067_S_AT; 21624 217767_AT; 218232_ GO Biological immune response 38 272 725 12602 8.13e-007 200986_AT; 202357_ Process 202953_AT; 202988_ 203381_S_AT; 20338 204533_AT; 204606_ 204897_AT; 205392_ 208078_S_AT; 20845 208791_AT; 208792_ 208961_S_AT; 20968 210163_AT; 210495_ 212067_S_AT; 21246 213958_AT; 216248_ 216598_S_AT; 21683 220423_AT; 225353_ 231124_X_AT GO Biological response to 29 272 465 12602 8.46e-007 200986_AT; 202357_ Process pest/pathogen/parasit 202992_AT; 203052_ e 204533_AT; 204606_ 205890_S_AT; 20629 208747_S_AT; 20879 209785_S_AT; 21007 211719_X_AT; 2120 216248_S_AT; 21644 217767_AT; 218232_ 228176_AT; 231124_

16 GO Biological defense response 40 272 815 12602 1.97e-006 200986_AT; 202357_ Process 202953_AT; 202988_ 203381_S_AT; 20338 204533_AT; 204606_ 204897_AT; 205392_ 208078_S_AT; 20845 208791_AT; 208792_ 208961_S_AT; 20960 209785_S_AT; 20979 210495_X_AT; 2117 212464_S_AT; 21288 216248_S_AT; 21644 216834_AT; 217767_ 225353_S_AT; 22564 GO Biological cell adhesion 32 272 597 12602 4.86e-006 200771_AT; 201505_ Process 202112_AT; 202202_ 202404_S_AT; 20287 203868_S_AT; 20416 206134_AT; 206295_ 209687_AT; 209795_ 211719_X_AT; 2119 212464_S_AT; 21271 213958_AT; 216442_ 217890_S_AT; 22190 231124_X_AT GO Biological response to biotic 41 272 884 12602 5.65e-006 200986_AT; 202357_ Process stimulus 202953_AT; 202988_ 203381_S_AT; 20338 203915_AT; 204517_ 204621_S_AT; 20462 205392_S_AT; 20589 208078_S_AT; 20845 208791_AT; 208792_ 208961_S_AT; 20960 209785_S_AT; 20979 210495_X_AT; 2117 212464_S_AT; 21288 216248_S_AT; 21644 216834_AT; 217767_ 225353_S_AT; 22564 GO Biological response to stress 38 272 824 12602 1.57e-005 200986_AT; 201058_ Process 202357_S_AT; 20287 203052_AT; 203381_ 203454_S_AT; 20372 204533_AT; 204606_ 205890_S_AT; 20629 207714_S_AT; 20845 208791_AT; 208792_ 210072_AT; 210163_ 211719_X_AT; 2120 212225_AT; 212227_ 212884_X_AT; 2162 216598_S_AT; 21776 221563_AT; 225353_ 231124_X_AT; 3702

17 Table 4S. Genes differentially expressed in AILT vs. PTCL/U and ALCL

Down- Gene Common GeneBank Description regulation (Z score)

2.611 202376_at SERPINA3 NM_001085 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3

2.247 206108_s_at SFRS6 NM_006275 splicing factor, arginine/serine-rich 6 2.189 225575_at LIFR AI680541 leukemia inhibitory factor receptor 2.037 227271_at FGF11 AU151265 fibroblast growth factor 11 1.891 225283_at ARRDC4 AV701177 arrestin domain containing 4 1.766 207735_at RNF125 NM_017831 ring finger protein 125 1.687 205378_s_at ACHE NM_015831 acetylcholinesterase (YT blood group) 1.686 202725_at POLR2A NM_000937 polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 1.642 200606_at DSP NM_004415 1.617 201746_at TP53 NM_000546 tumor protein (Li-Fraumeni syndrome) 1.609 209121_x_at NR2F2 M64497 nuclear receptor subfamily 2, group F, member 2 1.594 228854_at ZNF145 AI492388 zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia) 1.566 205326_at RAMP3 NM_005856 receptor (calcitonin) activity modifying protein 3 1.556 221748_s_at TNS AL046979 tensin 1.552 207289_at MMPL1 NM_004142 matrix metalloproteinase 25 1.535 210060_at PDE6G M36476 phosphodiesterase 6G, cGMP-specific, rod, gamma 1.532 1560476_at AF290476 Homo sapiens clone 38-1G2, mRNA sequence.

1.521 202221_s_at EP300 AV727101 AV727101 HTC Homo sapiens cDNA clone HTCBGF05 5', mRNA sequence. 1.521 204953_at SNAP91 NM_014841 1.516 226716_at KIAA1205 AB033031 KIAA1205 1.508 220975_s_at C1QTNF1 NM_030968 C1q and tumor necrosis factor related protein 1

1.463 229024_at BF056892 CDNA FLJ10151 fis, clone HEMBA1003402

1.461 242657_at AI078033 Transcribed sequence with weak similarity to protein ref:NP_060219.1 (H.sapiens) hypothetical protein FLJ20294 [Homo sapiens]

1.451 216348_at RPS17 AL049693 1.44 225288_at COL27A1 AI949136 collagen, type XXVII, alpha 1 1.433 1565763_at FLJ14834 AA137014 hypothetical protein FLJ14834 1.403 215372_x_at AU146794 MRNA; cDNA DKFZp686P13243 (from clone DKFZp686P13243) 1.391 1555523_a_at FYCO1 BC007218 FYVE and coiled-coil domain containing 1 1.378 215116_s_at DNM1 AF035321 1 1.362 229902_at LOC285682 AW083785 fms-related tyrosine kinase 4 1.355 213131_at OLFM1 R38389 yc96b12.s1 Soares infant brain 1NIB Homo sapiens cDNA clone IMAGE:23744 3', mRNA sequence.

18 1.341 214246_x_at MINK AI859060 wl66d06.x1 NCI_CGAP_Brn25 Homo sapiens cDNA clone IMAGE:2429867 3', mRNA sequence. 1.337 1567622_at ABLIM2 AJ431609 actin binding LIM , member 2 1.321 1564224_x_at LOC283314 AK091792 hypothetical protein LOC283314 1.319 220559_at EN1 NM_001426 homolog 1 1.299 212664_at TUBB5 AL567012 tubulin, beta, 5 1.279 212793_at DAAM2 BF513244 dishevelled associated activator of morphogenesis 2 1.256 226913_s_at SOX8 BF527050 602039960F2 NCI_CGAP_Brn67 Homo sapiens cDNA clone IMAGE:4177598 5', mRNA sequence. 1.25 1557611_at TTLL4 AW779022 tubulin tyrosine ligase-like family, member 4

1.246 204273_at EDNRB NM_000115 endothelin receptor type B 1.226 218983_at C1RL NM_016546 complement component 1, r subcomponent-like

1.219 230682_x_at ABCC3 BF515888 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 1.217 232935_at AA569225 MRNA; cDNA DKFZp686K13109 (from clone DKFZp686K13109) 1.214 230081_at AI694325 Similar to RIKEN cDNA B130016O10 gene (LOC345557), mRNA 1.2 227870_at NOPE AB046848 likely ortholog of mouse neighbor of Punc E11 1.199 219064_at ITIH5 NM_030569 inter-alpha (globulin) inhibitor H5 1.198 244324_at MGC33382 BG283921 602407676F1 NIH_MGC_91 Homo sapiens cDNA clone IMAGE:4519747 5', mRNA sequence. 1.195 227239_at DRCTNNB1A AV734839 AV734839 cdA Homo sapiens cDNA clone cdAAHD06 5', mRNA sequence. 1.188 224562_at WASF2 AK025566 WAS protein family, member 2 1.188 35147_at MCF2L AB002360 MCF.2 cell line derived transforming sequence- like 1.18 231106_at LOC255326 AI684591 CDNA clone IMAGE:4648334, partial cds 1.176 212875_s_at C21orf25 AP001745 1.169 205970_at MT3 NM_005954 metallothionein 3 (growth inhibitory factor (neurotrophic)) 1.165 224970_at NFIA AA419275 zv35e01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone IMAGE:755640 3', mRNA sequence. 1.162 52651_at COL8A2 AI806793 collagen, type VIII, alpha 2 1.155 233383_at AU156482 AU156482 PLACE1 Homo sapiens cDNA clone PLACE1003528 3', mRNA sequence.

1.15 221636_s_at FLJ20605 AL136931 hypothetical protein FLJ20605 1.141 206540_at GLB1L NM_024506 galactosidase, beta 1-like 1.135 227318_at AL359605 CDNA FLJ42883 fis, clone BRHIP3006683 1.129 207016_s_at ALDH1A2 AB015228 aldehyde dehydrogenase 1 family, member A2

1.121 235221_at R52665 yg99a07.s1 Soares infant brain 1NIB Homo sapiens cDNA clone IMAGE:41525 3', mRNA sequence. 1.12 233158_at KRTHB2 AI082251 , hair, basic, 2 1.095 205876_at LIFR NM_002310 leukemia inhibitory factor receptor

19 1.091 202222_s_at DES NM_001927 1.085 211677_x_at IGSF4B AF062733 immunoglobulin superfamily, member 4B 1.084 1554219_at MGC34919 BC027448 hypothetical protein MGC34919 1.084 214683_s_at CLK1 AI251890 CDC-like kinase 1 1.082 208871_at DRPLA D31840 dentatorubral-pallidoluysian atrophy (atrophin- 1) 1.081 212494_at TENC1 AB028998 tensin like C1 domain containing phosphatase

1.079 239270_at AL133721 Similar to RIKEN cDNA B130016O10 gene (LOC345557), mRNA 1.074 238904_at D60432 HUM108B01A Clontech human fetal brain polyA+ mRNA (#6535) Homo sapiens cDNA clone GEN-108B01 3', mRNA sequence.

1.068 222802_at EDN1 J05008 Homo sapiens endothelin-1 (EDN1) gene, complete cds. 1.068 226304_at HSPB6 AA563621 hypothetical protein FLJ32389 1.063 225355_at DKFZP761M1511 AK026748 hypothetical protein DKFZP761M1511 1.062 234345_at AL157439 MRNA; cDNA DKFZp434A225 (from clone DKFZp434A225) 1.054 206377_at FOXF2 NM_001452 forkhead box F2 1.052 226911_at FLJ39155 BF114725 hypothetical protein FLJ39155 1.03 219511_s_at SNCAIP NM_005460 synuclein, alpha interacting protein (synphilin)

1.023 1562067_at BC042865 Clone IMAGE:5312957, mRNA 1.011 221850_x_at CTGLF1 AI826075 ARF GTPase-activating protein, mRNA (cDNA clone IMAGE:5811925), partial cds 0.997 233079_at AK026802 CDNA: FLJ23149 fis, clone LNG09335 0.993 1554420_at ATF3 AB078026 activating transcription factor 3 0.982 209343_at EFHD1 BC002449 EF hand domain containing 1 0.969 232861_at PDP2 AB037769 pyruvate dehydrogenase phosphatase isoenzyme 2 0.947 1553243_at FLJ14641 NM_032817 hypothetical protein FLJ14641 0.92 222167_at AK021836 MRNA; cDNA DKFZp686H14239 (from clone DKFZp686H14239) 0.908 203178_at GATM NM_001482 glycine amidinotransferase (L-arginine:glycine amidinotransferase) 0.88 202060_at SH2BP1 NM_014633 SH2 domain binding protein 1 (tetratricopeptide repeat containing) 0.714 210135_s_at SHOX2 AF022654 short stature homeobox 2

20 Table 5S. Genes differentially expressed in AILT vs. PTCL/U

Down- Gene Common GeneBank Description regulation (Z score) 4.73 210072_at CCL19 U88321 chemokine (C-C motif) ligand 19 3.598 208581_x_at MT1X NM_005952 metallothionein 1X 3.35 212185_x_at MT2A NM_005953 metallothionein 2A 3.278 217165_x_at MT2A M10943 human metallothionein-If; Human metallothionein-If gene (hMT-If). 3.242 1555653_at hnRNPA3 BC012090 3.005 218345_at HCA112 NM_018487 hepatocellular carcinoma-associated antigen 112

2.997 204326_x_at MT1X NM_002450 2.987 206461_x_at MT1H NM_005951 metallothionein 1H 2.98 220532_s_at LR8 NM_014020 LR8 protein 2.967 212859_x_at MT1E BF217861 metallothionein 2A 2.929 36994_at ATP6V0C M62762 Human vacuolar H+ ATPase proton channel subunit mRNA, complete cds. 2.845 217767_at C3 NM_000064 complement component 3 2.775 208540_x_at S100A11 NM_021039 2.646 206662_at GLRX NM_002064 glutaredoxin (thioltransferase) 2.638 202376_at SERPINA3 NM_001085 serine (or cysteine) proteinase inhibitor, clade A (alpha- 1 antiproteinase, antitrypsin), member 3

2.558 200675_at CD81 NM_004356 CD81 antigen (target of antiproliferative antibody 1)

2.514 206108_s_at SFRS6 NM_006275 splicing factor, arginine/serine-rich 6 2.453 213629_x_at MT1F BF246115 metallothionein 1F (functional) 2.385 204745_x_at MT1G NM_005950 metallothionein 1G 2.361 1558836_at BQ024490 UI-1-BB1p-aut-f-08-0-UI.s1 NCI_CGAP_Pl6 Homo sapiens cDNA clone UI-1-BB1p-aut-f-08-0-UI 3', mRNA sequence. 2.273 224583_at COTL1 AL565621 coactosin-like 1 (Dictyostelium) 2.249 212884_x_at APOE AI358867 apolipoprotein E 2.202 202727_s_at IFNGR1 NM_000416 interferon gamma receptor 1 2.199 215235_at SPTAN1 AL110273 , alpha, non-erythrocytic 1 (alpha-fodrin)

2.15 234987_at AV715309 Similar to dJ132F21.2 (Contains a novel protein similar to the L82E from Drosophila) (LOC343574), mRNA

2.146 221477_s_at MGC5618 BF575213 superoxide dismutase 2, mitochondrial 2.124 200782_at ANXA5 NM_001154 annexin A5 2.093 207460_at GZMM NM_005317 granzyme M (lymphocyte met-ase 1) 2.075 211509_s_at RTN4 AB015639 reticulon 4 2.063 212171_x_at VEGF H95344 vascular endothelial growth factor 2.051 1558837_a_at BQ024490 UI-1-BB1p-aut-f-08-0-UI.s1 NCI_CGAP_Pl6 Homo sapiens cDNA clone UI-1-BB1p-aut-f-08-0-UI 3', mRNA sequence. 2.043 212303_x_at KHSRP BG026366 602291736F1 NIH_MGC_86 Homo sapiens cDNA clone IMAGE:4386489 5', mRNA sequence.

2.024 200945_s_at SEC31L1 NM_014933 SEC31-like 1 (S. cerevisiae)

21 2.01 201425_at ALDH2 NM_000690 aldehyde dehydrogenase 2 family (mitochondrial)

2.001 64064_at IAN4L1 AI435089 th95b11.x1 Soares_NSF_F8_9W_OT_PA_P_S1 Homo sapiens cDNA clone IMAGE:2126397 3', mRNA sequence.

1.974 227853_at AW024350 Transcribed sequence with weak similarity to protein pir:I60307 (E. coli) I60307 beta-galactosidase, alpha peptide - Escherichia coli 1.967 221747_at TNS AL046979 tensin 1.967 224927_at KIAA1949 BG251556 KIAA1949 1.955 206359_at SOCS3 BG035761 suppressor of cytokine signaling 3 1.949 240991_at AI732596 Transcribed sequence with weak similarity to protein ref:NP_060265.1 (H.sapiens) hypothetical protein FLJ20378 [Homo sapiens] 1.891 217892_s_at EPLIN NM_016357 epithelial protein lost in neoplasm beta 1.875 200800_s_at HSPA1A NM_005345 heat shock 70kDa protein 1A 1.873 202759_s_at AKAP2 BE879367 paralemmin 2 1.844 202794_at INPP1 NM_002194 inositol polyphosphate-1-phosphatase 1.834 204858_s_at ECGF1 NM_001953 endothelial cell growth factor 1 (platelet-derived)

1.829 231241_at AW469714 Transcribed sequence with moderate similarity to protein ref:NP_055224.1 (H.sapiens) PCAF associated factor 65 beta [Homo sapiens] 1.827 204166_at KIAA0963 NM_014963 1.825 213733_at MYO1F BF740152 myosin IF 1.82 234973_at SLC38A5 BG325630 solute carrier family 38, member 5 1.816 209003_at SLC25A11 AF070548 solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11 1.815 201862_s_at LRRFIP1 NM_004735 leucine rich repeat (in FLII) interacting protein 1

1.809 221489_s_at SPRY4 W48843 sprouty homolog 4 (Drosophila) 1.805 201042_at TGM2 AL031651 1.783 209758_s_at MFAP5 U37283 Microfibril-associated glycoprotein-2 1.771 218094_s_at C20orf35 NM_018478 chromosome 20 open reading frame 35 1.766 200035_at DULLARD NM_015343 GABA(A) receptor-associated protein 1.748 212527_at D15Wsu75e BF057059 DNA segment, Chr 15, Wayne State University 75, expressed 1.733 223054_at DNAJB11 BC001144 DnaJ (Hsp40) homolog, subfamily B, member 11

1.718 221484_at B4GALT5 BF691447 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 1.711 204135_at DOC1 NM_014890 downregulated in ovarian cancer 1 1.694 212501_at CEBPB AL564683 AL564683 Homo sapiens FETAL LIVER Homo sapiens cDNA clone CS0DM007YK12 3-PRIME, mRNA sequence. 1.681 217762_s_at RAB31 BE789881 RAB31, member RAS oncogene family 1.647 225744_at ZDHHC8 AB033118 zinc finger, DHHC domain containing 8 1.64 209031_at IGSF4 AL519710 immunoglobulin superfamily, member 4 1.633 235306_at hIAN6 AI611648 tt37g06.x1 NCI_CGAP_GC6 Homo sapiens cDNA clone IMAGE:2243002 3' similar to contains MER13.t1 MER13 repetitive element ;, mRNA sequence.

1.62 224215_s_at DLL1 AF196571 delta-like 1 (Drosophila)

22 1.56 215645_at FLJ11286 AF090883 hypothetical protein FLJ11286 1.525 209508_x_at CFLAR AF005774 CASP8 and FADD-like apoptosis regulator 1.516 202249_s_at H326 AU146233 H326 1.51 242403_at AI459177 Transcribed sequence with moderate similarity to protein sp:P39194 (H.sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry

1.482 242738_s_at ATBF1 BG402859 602418552F1 NIH_MGC_93 Homo sapiens cDNA clone IMAGE:4525500 5', mRNA sequence.

1.48 215909_x_at MINK AL157418 Homo sapiens mRNA; cDNA DKFZp761K18121 (from clone DKFZp761K18121).

1.462 205323_s_at MTF1 NM_005955 metal-regulatory transcription factor 1 1.451 1552318_at IMAP1 AK091818 immunity associated protein 1 1.441 220091_at SLC2A6 NM_017585 solute carrier family 2 (facilitated glucose transporter), member 6 1.418 213817_at AL049435 MRNA; cDNA DKFZp586B0220 (from clone DKFZp586B0220) 1.392 206486_at LAG3 NM_002286 lymphocyte-activation gene 3 1.351 225415_at BBAP AA577672 rhysin 2 -1.224 1555743_s_at U92816 Homo sapiens c33.6 unnamed HERV-H protein mRNA, complete cds. -1.244 243963_at SDCCAG8 AI473707 serologically defined colon cancer antigen 8

23