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Supplement, Table 1 Supplement, Table 4. Genes identified by SAM as differentially expressed in primary and follow-up biopsies of Celecoxibe-treated patients Fold- UniGene SAM Geneb Clone difference p-valuec cluster Rank P/Fa collagen, type X, alpha 1(Schmid metaphyseal chondrodysplasia) IncytePD:4855492 Hs.179729 2.061 0.00004 9 dual adaptor of phosphotyrosine and 3-phosphoinositides IncytePD:1304879 Hs.62643 1.989 0.00000 1 immunoglobulin superfamily, member 6 IncytePD:522893 Hs.135194 1.964 0.00003 2 ATP-binding cassette, sub-family B (MDR/TAP), member 1 IncytePD:1931381 Hs.21330 1.938 0.00002 21 Homo sapiens transcribed sequences IncytePD:4073268 Hs.133181 1.899 0.00024 22 Homo sapiens transcribed sequences IncytePD:3846507 Hs.443475 1.888 0.00013 5 heparin-binding growth factor binding protein IncytePD:2024613 Hs.1690 1.885 0.00032 11 caspase 8, apoptosis-related cysteine protease IncytePD:2466440 Hs.243491 1.884 0.00032 44 platelet activating receptor homolog IncytePD:3879095 Hs.159545 1.882 0.00070 54 interleukin 22 receptor, alpha 1 IncytePD:3257185 Hs.110915 1.879 0.00015 10 chromosome 4 open reading frame 7 IncytePD:968141 Hs.320147 1.879 0.00592 522 carbonic anhydrase I IncytePD:2101663 Hs.23118 1.865 0.00001 4 diacylglycerol kinase, beta 90kDa IncytePD:1213571 Hs.158318 1.843 0.00003 15 Homo sapiens similar to BET1 homolog (Golgi vesicular membrane trafficking protein p18) (hBET1) (LOC378412), mRNA IncytePD:1534801 Hs.395787 1.836 0.01066 217 TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56) IncytePD:1907369 1.825 0.00010 24 potassium inwardly-rectifying channel, subfamily J, member 2 IncytePD:630604 Hs.1547 1.815 0.00005 8 membrane-spanning 4-domains, subfamily A, member 1 IncytePD:2313368 Hs.438040 1.814 0.03133 768 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) IncytePD:3473060 Hs.502 1.812 0.00621 59 colipase, pancreatic IncytePD:2383235 Hs.1340 1.795 0.00157 63 tubby homolog (mouse) IncytePD:5092727 Hs.54468 1.789 0.00309 87 vanin 1 IncytePD:3843507 Hs.12114 1.785 0.01707 167 chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) IncytePD:950310 Hs.164021 1.769 0.00000 25 Homo sapiens transcribed sequences IncytePD:2289203 Hs.49132 1.764 0.00081 50 KIAA0802 protein IncytePD:5043515 Hs.434101 1.761 0.00236 20 histidine-rich glycoprotein IncytePD:2517389 Hs.1498 1.754 0.00117 113 Incyte EST IncytePD:2496526 1.751 0.00254 61 Homo sapiens mRNA; cDNA DKFZp686H0155 (from clone DKFZp686H0155) IncytePD:2906194 Hs.513302 1.747 0.00002 27 CD3D antigen, delta polypeptide (TiT3 complex) IncytePD:3297914 Hs.95327 1.743 0.00384 141 keratin, hair, acidic, 3B IncytePD:3187903 Hs.32950 1.741 0.00021 55 Down syndrome cell adhesion molecule IncytePD:4774130 Hs.49002 1.739 0.00026 32 interleukin 9 receptor IncytePD:2211721 1.731 0.00019 37 progestagen-associated endometrial protein (placental protein 14, pregnancy-associated endometrial alpha-2-globulin, alpha uterine protein) IncytePD:1976179 Hs.82269 1.728 0.00063 43 early growth response 4 IncytePD:1902066 Hs.3052 1.722 0.00212 39 lymphotoxin beta (TNF superfamily, member 3) IncytePD:508631 Hs.376208 1.719 0.00429 155 agrin IncytePD:4610962 Hs.273330 1.71 0.00045 120 lymphotoxin beta (TNF superfamily, member 3) IncytePD:736669 1.71 0.02676 477 SH2 domain protein 1A, Duncan's disease (lymphoproliferative syndrome) IncytePD:2936016 Hs.151544 1.683 0.02605 354 Homo sapiens mRNA; cDNA DKFZp686P24244 (from clone DKFZp686P24244) IncytePD:1638327 Hs.119065 1.665 0.00002 12 ring finger protein 128 IncytePD:1365975 Hs.9238 1.655 0.00118 66 prostaglandin I2 (prostacyclin) receptor (IP) IncytePD:663798 Hs.458324 1.652 0.00023 34 retinoic acid receptor responder (tazarotene induced) 3 IncytePD:1927347 Hs.17466 1.647 0.00030 49 chromosome X open reading frame 9 IncytePD:1221280 Hs.61469 1.629 0.01379 222 Homo sapiens cDNA FLJ26466 fis, clone KDN04258 IncytePD:1813721 Hs.447683 1.622 0.00492 36 solute carrier family 6 (neurotransmitter transporter, GABA), member 13 IncytePD:2102890 Hs.126852 1.621 0.00722 194 chimerin (chimaerin) 2 IncytePD:3220181 Hs.407520 1.62 0.00581 278 Homo sapiens clone 23583 mRNA sequence IncytePD:3321366 Hs.12509 1.619 0.00107 19 adlican IncytePD:1402105 Hs.72157 1.618 0.00018 33 indoleamine-pyrrole 2,3 dioxygenase IncytePD:1749102 Hs.840 1.613 0.01720 812 KH-type splicing regulatory protein (FUSE binding protein 2) IncytePD:3460518 Hs.91142 1.612 0.00091 18 matrix metalloproteinase 12 (macrophage elastase) IncytePD:1563275 Hs.1695 1.607 0.00823 247 small inducible cytokine subfamily C, member 1 (lymphotactin) IncytePD:308896 1.6 0.00006 56 granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) IncytePD:1876511 Hs.1051 1.596 0.00322 185 hypothetical protein LOC89958 IncytePD:2238576 Hs.19322 1.595 0.00018 17 Homo sapiens transcribed sequences IncytePD:1916844 Hs.102728 1.595 0.00632 164 ras homolog gene family, member F (in filopodia) IncytePD:1905723 Hs.512618 1.594 0.00001 3 regulator of G-protein signalling 13 IncytePD:3696625 Hs.17165 1.594 0.01576 791 receptor (calcitonin) activity modifying protein 1 IncytePD:1803793 Hs.32989 1.593 0.00205 264 purinergic receptor P2Y, G-protein coupled, 1 IncytePD:1961218 Hs.2411 1.586 0.00036 241 solute carrier family 22 (organic cation transporter), member 2 IncytePD:4337804 Hs.436385 1.585 0.00161 385 copine VI (neuronal) IncytePD:2284107 Hs.6132 1.585 0.00035 14 unc-5 homolog C (C. elegans) IncytePD:3350064 Hs.125605 1.582 0.00043 26 neuropeptide Y receptor Y2 IncytePD:3630683 Hs.37125 1.58 0.01391 560 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F IncytePD:1296442 Hs.32981 1.578 0.00880 121 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein) IncytePD:1311071 Hs.151449 1.577 0.00968 372 spectrin, beta, erythrocytic (includes spherocytosis, clinical type I) IncytePD:2189383 Hs.438514 1.574 0.00028 35 aminocarboxymuconate semialdehyde decarboxylase IncytePD:4073445 Hs.114088 1.573 0.00900 661 Incyte EST IncytePD:2895226 1.573 0.00378 585 hemogen IncytePD:680 Hs.176626 1.572 0.00109 153 EphA2 IncytePD:1958394 Hs.171596 1.571 0.00205 98 trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) IncytePD:963536 1.57 0.02591 334 sodium channel, voltage-gated, type VII, alpha IncytePD:3960518 Hs.406684 1.568 0.00321 48 VENT-like homeobox 2 IncytePD:2023264 Hs.125231 1.565 0.00107 41 hypothetical protein DKFZp667E0512 IncytePD:1214652 Hs.432998 1.563 0.00005 16 Homo sapiens mRNA; cDNA DKFZp564B076 (from clone DKFZp564B076) IncytePD:767447 Hs.21103 1.56 0.00060 71 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2 IncytePD:557012 Hs.75716 1.559 0.02405 432 Homo sapiens transcribed sequence with weak similarity to protein ref:NP_060190.1 (H.sapiens) hypothetical protein FLJ20234 [Homo sapiens] IncytePD:1425124 Hs.380046 1.558 0.00135 104 baculoviral IAP repeat-containing 3 IncytePD:1603857 Hs.127799 1.557 0.00358 161 arginase, liver IncytePD:166337 1.55 0.00338 182 chymotrypsin C (caldecrin) IncytePD:4079043 Hs.8709 1.547 0.01566 446 solute carrier family 2 (facilitated glucose transporter), member 2 IncytePD:2923154 Hs.167584 1.546 0.00908 232 epithelial V-like antigen 1 IncytePD:1824332 Hs.116651 1.546 0.00260 96 lymphocyte-specific protein tyrosine kinase IncytePD:3031058 Hs.1765 1.546 0.00442 101 dickkopf homolog 1 (Xenopus laevis) IncytePD:5047895 Hs.40499 1.541 0.02225 380 SH3 and multiple ankyrin repeat domains 2 IncytePD:2875308 Hs.12696 1.541 0.01159 144 DNA segment on chromosome 6 (unique) 49 expressed sequence IncytePD:2102881 1.536 0.00024 28 chromodomain helicase DNA binding protein 3 IncytePD:1965248 Hs.25601 1.534 0.03771 482 sodium channel, nonvoltage-gated 1, delta IncytePD:3276284 Hs.512681 1.534 0.01878 83 hydroxyprostaglandin dehydrogenase 15-(NAD) IncytePD:1578941 Hs.77348 1.533 0.02005 406 likely ortholog of mouse zinc finger protein EZI IncytePD:1336756 Hs.112158 1.533 0.00276 73 putative purinergic receptor IncytePD:2438496 1.533 0.05122 618 proline-rich protein BstNI subfamily 2 IncytePD:1326702 Hs.283658 1.532 0.01438 370 Incyte EST IncytePD:637290 1.529 0.00095 65 aldehyde dehydrogenase 8 family, member A1 IncytePD:2043488 Hs.18443 1.528 0.00519 91 CD1C antigen, c polypeptide IncytePD:932244 Hs.1311 1.527 0.02639 388 opioid binding protein/cell adhesion molecule-like IncytePD:3599458 Hs.4817 1.524 0.00782 51 keratin 20 IncytePD:1734393 Hs.84905 1.524 0.00308 154 defensin, beta 1 IncytePD:2912830 Hs.32949 1.523 0.00220 90 osteoblast specific factor 2 (fasciclin I-like) IncytePD:1924486 Hs.136348 1.521 0.01140 259 glutamate receptor, ionotrophic, AMPA 3 IncytePD:1368760 Hs.377070 1.519 0.00121 60 kallikrein 1, renal/pancreas/salivary IncytePD:1327263 Hs.123107 1.514 0.01035 246 cystatin A (stefin A) IncytePD:1821453 Hs.412999 1.513 0.00393 235 interferon, beta 1, fibroblast IncytePD:4906826 Hs.93177 1.513 0.02236 364 prostate derived STE20-like kinase PSK IncytePD:4326355 Hs.122823 1.511 0.00765 234 cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) IncytePD:2740235 Hs.421349 1.508 0.00807 267 Incyte EST IncytePD:2060021 1.508 0.00230 140 solute carrier family 18 (vesicular monoamine), member 1 IncytePD:3494716 Hs.158322 1.504 0.00418 271 retinoic acid induced 3 IncytePD:899118 Hs.194691 1.503 0.00074 62 protein phosphatase 1, regulatory (inhibitor) subunit 16B IncytePD:1678639 Hs.45719 1.501 0.00028 23 TIR domain containing adaptor inducing interferon-beta IncytePD:614996 Hs.29344 1.5 0.00311 117 interferon,
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