Table 1.
TheTop 93 Deregulated Genes in Barrett's Adenocarcinomas
| Tag sequence | UniGene cluster ID | Gene symbol | Title | Location | T4 tag count | N4 tag count | Ratio, T4/N4 | P value |
|---|---|---|---|---|---|---|---|---|
| Upregulated genes | ||||||||
| GTGGCCACGG | Hs.112405 | S100A9 | S100 calcium binding protein A9 | 1q21 | 355 | 0 | 418 | ≤0.001 |
| GAGCAGCGCC | Hs.112408 | S100A7 | S100 calcium binding protein A7 | 1q21 | 95 | 0 | 112 | ≤0.001 |
| AAGATTGGTG | Hs.114286 | CD9 | CD9 antigen (p24) | 12p13.3 | 112 | 7 | 10 | ≤0.001 |
| GCACCTGTCG | Hs.1239 | ANPEP | Alanyl (membrane) aminopeptidase | 15q25‐q26 | 76 | 0 | 89 | ≤0.001 |
| GTGACAGAAG | Hs.129673 | EIF4A1 | Eukaryotic translation initiation factor 4A, isoform 1 | 17p13 | 92 | 4 | 14 | ≤0.001 |
| TTTCCTGCTC | Hs.139322 | SPRR3 | Small proline‐rich protein 3 | 1q21‐q22 | 308 | 0 | 362 | ≤0.001 |
| GTTCAAGTGA | Hs.186810 | REPS2 | RALBP1 associated Eps domain containing 2 | Xp22.2 | 107 | 2 | 32 | ≤0.001 |
| ACTGTATTTT | Hs.194691 | Hs.194691 | G protein‐coupled receptor, family C, group 5, member A | 12p13‐p12.3 | 103 | 6 | 10 | ≤0.001 |
| TGGATCCTGA | Hs.302145 | HBG2 | Hemoglobin, gamma G | 11p15.5 | 75 | 0 | 88 | ≤0.001 |
| CAGGAGGAGT | Hs.308709 | GRP58 | Protein disulfide isomerase family A, member 3 | 15q15 | 81 | 2 | 24 | ≤0.001 |
| CTAGTCTTTG | Hs.353175 | AGPAT4 | 1‐acylglycerol‐3‐phosphate O‐acyltransferase 4 | 6q26 | 85 | 0 | 100 | ≤0.001 |
| TCACCCAGGG | Hs.391464 | ABCC1 | ATP‐binding cassette, subfamily C member 1 | 16p13.1 | 52 | 0 | 61 | ≤0.001 |
| CCTGGTCCCA | Hs.411501 | KRT7 | Keratin 7 | 12q12‐q13 | 179 | 1 | 106 | ≤0.001 |
| TTCTTTCTAA | Hs.411925 | TMEM38B | Transmembrane protein 38B | 9q31.2 | 58 | 1 | 34 | ≤0.001 |
| TACCTGCAGA | Hs.416073 | S100A8 | S100 calcium binding protein A8 | 1q21 | 343 | 1 | 204 | ≤0.001 |
| CAGCAGAAGC | Hs.424126 | SERF2 | Small EDRK‐rich factor 2 | 15q15.3 | 79 | 4 | 12 | ≤0.001 |
| GCGGCGGATG | Hs.445351 | LGALS1 | Lectin, galactoside‐binding, soluble, 1 | 22q13.1 | 89 | 0 | 105 | ≤0.001 |
| GAACATTGCA | Hs.447579 | LOC339290 | Hypothetical protein LOC339290 | 18p11.31 | 95 | 0 | 112 | ≤0.001 |
| GTTTGGGTTG | Hs.459927 | PTMA | Prothymosin, alpha (gene sequence 28) | 2q35‐q36 | 162 | 9 | 11 | ≤0.001 |
| TCACCCACAC | Hs.462859 | SCFD2 | Short‐chain dehydrogenase/reductase | 17q12 | 337 | 31 | 6 | ≤0.001 |
| CCCCCGCGGA | Hs.466507 | LISCH7 | Liver‐specific bHLH‐Zip transcription factor | 19q13.12 | 48 | 0 | 56 | ≤0.001 |
| CGGAGACCCT | Hs.473583 | NSEP1 | Y box binding protein 1 | 1p34 | 76 | 2 | 23 | ≤0.001 |
| GCCGGGTGGG | Hs.501293 | BSG | Basigin (OK blood group) | 19p13.3 | 77 | 4 | 11 | ≤0.001 |
| GATACTTGGA | Hs.501911 | GALNTL4 | Casein kinase 2, alpha 1 polypeptide | 11p15.3 | 94 | 0 | 111 | ≤0.001 |
| ACAGGCTACG | Hs.503998 | TAGLN | Transgelin | 11q23.2 | 71 | 3 | 14 | ≤0.001 |
| GTGGCTCACA | Hs.504820 | MGC14817 | Hypothetical protein MGC14817 | 12q14.3 | 242 | 16 | 9 | ≤0.001 |
| TAATTTTTGC | Hs.508113 | OLFM4 | Olfactomedin 4 | 13q14.3 | 228 | 1 | 136 | ≤0.001 |
| GTGAGCCCAT | Hs.509736 | HSPCB | Heat shock 90 kDa protein 1, beta | 6p12 | 149 | 13 | 7 | ≤0.001 |
| TGTCAGTCTG | Hs.512350 | Hs.512350 | LOC440676 | 1q21.1 | 108 | 1 | 64 | ≤0.001 |
| AGTGCAGGGC | Hs.512488 | Hs.512488 | Similar to 60S ribosomal protein L10 | 12q21.2 | 98 | 1 | 58 | ≤0.001 |
| GCGACCGTCA | Hs.513490 | ALDOA | Aldolase A, fructose‐bisphosphate | 16q22‐q24 | 206 | 4 | 31 | ≤0.001 |
| ACCGCCGTGG | Hs.513803 | CYBA | Cytochrome b‐245, alpha polypeptide | 16q24 | 77 | 0 | 91 | ≤0.001 |
| AGCAGGAGCA | Hs.515714 | S100A16 | S100 calcium binding protein A16 | 1q21 | 61 | 0 | 72 | ≤0.001 |
| GATCTCTTGG | Hs.516484 | S100A2 | S100 calcium binding protein A2 | 1q21 | 61 | 0 | 72 | ≤0.001 |
| ATCGTGGCGG | Hs.520942 | CLDN4 | Claudin 4 | 7q11.23 | 62 | 0 | 73 | ≤0.001 |
| CCCAAGCTAG | Hs.520973 | HSPB1 | Heat shock 27 kDa protein 1 | 7q11.23 | 175 | 7 | 15 | ≤0.001 |
| AACATTCGCA | Hs.523302 | PRDX3 | Peroxiredoxin 3 | 10q25‐q26 | 46 | 0 | 54 | ≤0.001 |
| CTTCTCATCT | Hs.531719 | ADCYAP1 | Adenylate cyclase activating polypeptide 1 | 18p11 | 85 | 1 | 51 | ≤0.001 |
| AACTGAGGGG | Hs.5333 | KIAA0711 | Kelch repeat and BTB (POZ) domain containing 11 | 8p23.3 | 94 | 0 | 111 | ≤0.001 |
| GACTCTTCAG | Hs.534293 | SERPINA3 | Serpin peptidase inhibitor, clade A member 3 | 14q32.1 | 125 | 1 | 74 | ≤0.001 |
| CATCGCCAGT | Hs.54483 | NMI | N‐myc (and STAT) interactor | 2p24.3‐q21.3 | 285 | 0 | 335 | ≤0.001 |
| GACGGCGCAG | Hs.546251 | ECGF1 | Endothelial cell growth factor 1 | 22q13 | 46 | 0 | 54 | ≤0.001 |
| TAGCTTTAAA | Hs.554202 | SVIL | Supervillin | 10p11.2 | 210 | 0 | 247 | ≤0.001 |
| TGGCCATCTG | Hs.555971 | PP1201 | Transmembrane BAX inhibitor motif containing 1 | 2p24.3‐p24.1 | 90 | 1 | 54 | ≤0.001 |
| CTATCCTCTC | Hs.75227 | NDUFA9 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39 kDa | 12p13.3 | 51 | 0 | 60 | ≤0.001 |
| ACTGCCCGCT | Hs.81071 | ECM1 | Extracellular matrix protein 1 | 1q21 | 77 | 1 | 46 | ≤0.001 |
| Downregulated genes | ||||||||
| GAGAACCACT | Hs.110014 | GIF | Gastric intrinsic factor (vitamin B synthesis) | 11q13 | 0 | 87 | 0.010 | ≤0.001 |
| TTGCCCCTAC | Hs.128814 | CHIA | Chitinase, acidic | 1p13.1‐p21.3 | 7 | 185 | 0.020 | ≤0.001 |
| ACACAGCAAG | Hs.131603 | Hs.476965 | EMI domain containing 2 | 7q22.1 | 44 | 250 | 0.100 | ≤0.001 |
| ACCCTCCCCA | Hs.132087 | FLJ46299 | Kelch domain containing 6 | 3q21.3 | 0 | 35 | 0.024 | ≤0.001 |
| AACCTCCCCG | Hs.132858 | RAP1GDS1 | RAP1, GTP‐GDP dissociation stimulator 1 | 4q23‐q25 | 0 | 33 | 0.026 | ≤0.001 |
| CAGTGCCTCT | Hs.133539 | MAST4 | Microtubule associated serine/threonine kinase family member 4 | 5q12.3 | 1 | 51 | 0.010 | ≤0.001 |
| AACCTCCCAC | Hs.134074 | ARL2BP | Solute carrier family 35, member E1 | 19p13.11 | 1 | 42 | 0.010 | ≤0.001 |
| CTGGCCCTCG | Hs.162807 | TFF1 | Trefoil factor 1 | 21q22.3 | 95 | 174 | 0.3 | ≤0.001 |
| TTTAGGATGA | Hs.16757 | GDDR | Down‐regulated in gastric cancer GDDR | 2p13.3 | 5 | 474 | 0.010 | ≤0.001 |
| CACCCCTGAT | Hs.173724 | CKB | Creatine kinase, brain | 14q32 | 9 | 74 | 0.070 | ≤0.001 |
| GACCTCCCCA | Hs.178728 | MBD3 | Methyl‐CpG binding domain protein 3 | 19p13.3 | 2 | 64 | 0.020 | ≤0.001 |
| AGTGCTCTTC | Hs.1867 | PGC | Progastricsin (pepsinogen C) | 6p21.3‐p21.1 | 36 | 595 | 0.040 | ≤0.001 |
| CCATTCTGAA | Hs.209217 | ASTN2 | Astrotactin 2 | 9q33.1 | 0 | 24 | 0.035 | ≤0.001 |
| CAGTGCTTCC | Hs.220864 | CHD2 | Chromodomain helicase DNA binding protein 2 | 15q26 | 5 | 41 | 0.070 | ≤0.001 |
| GCTGGAGGAA | Hs.2681 | GAS | Gastrin | 17q21 | 0 | 100 | 0.009 | ≤0.001 |
| CACCTCCCCA | Hs.283739 | BE614337 | Ubiquilin 4 | 1q21 | 4 | 76 | 0.030 | ≤0.001 |
| AGCCTCCCCA | Hs.2859 | OPRL1 | Opiate receptor‐like 1 | 20q13.33 | 2 | 68 | 0.020 | ≤0.001 |
| AAATCCTGGG | Hs.2979 | TFF2 | Trefoil factor 2 (spasmolytic protein 1) | 21q22.3 | 62 | 1086 | 0.030 | ≤0.001 |
| GCAGGCTCCA | Hs.302131 | GHRL | Ghrelin precursor | 3p26‐p25 | 5 | 50 | 0.060 | ≤0.001 |
| TGCCAATTAA | Hs.307835 | PGM5 | Phosphoglucomutase 5 | 9p12‐q12 | 6 | 40 | 0.090 | ≤0.001 |
| CCCTGGAAGC | Hs.309288 | CUGBP2 | CUG triplet repeat, RNA binding protein 2 | 10p13 | 1 | 33 | 0.020 | ≤0.001 |
| CTGACTGTGC | Hs.36992 | ATP4A | ATPase, H+/K+ exchanging, alpha polypeptide | 19q13.1 | 10 | 384 | 0.020 | ≤0.001 |
| GTTTGCTTGC | Hs.370480 | ABCB7 | ATP‐binding cassette, sub‐family B (MDR/TAP), member 7 | Xq12‐q13 | 1 | 26 | 0.020 | ≤0.001 |
| AACCTCCTCA | Hs.386698 | C10orf27 | Chromosome 10 open reading frame 27 | 10q22.1 | 0 | 29 | 0.029 | ≤0.001 |
| TATATCAGTG | Hs.388654 | ATP6V1G1 | ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G isoform 1 | 9q32 | 3 | 48 | 0.040 | ≤0.001 |
| AACCTCCCCA | Hs.432854 | PGA5 | Porin, putative | 11q13 | 365 | 6637 | 0.030 | ≤0.001 |
| GGAACGCAAG | Hs.434202 | ATP4B | ATPase, H+/K+ exchanging, beta polypeptide | 13q34 | 4 | 138 | 0.020 | ≤0.001 |
| TCTCCATACC | Hs.438454 | FBXO25 | F‐box protein 25 | 8p23.3 | 12 | 376 | 0.020 | ≤0.001 |
| TCCCTTTAAG | Hs.438824 | CKIP‐1 | CK2 interacting protein 1 | 1q21.2 | 3 | 49 | 0.040 | ≤0.001 |
| TTTTTCAAGA | Hs.445586 | UNQ473 | DMC | 19q13.2 | 2 | 35 | 0.030 | ≤0.001 |
| CAGTGCTCTT | Hs.445680 | Hs.445680 | Similar to anaphase promoting complex subunit 1 | 2q12.3 | 1 | 42 | 0.010 | ≤0.001 |
| ACTGATCTGC | Hs.447547 | VPS35 | Hypothetical protein MGC34800 | 16q12 | 5 | 34 | 0.090 | ≤0.001 |
| TCATTTTGAA | Hs.464472 | MRCL3 | Myosin regulatory light chain MRLC2 | 18p11.31 | 0 | 27 | 0.031 | ≤0.001 |
| CAATGCTTCT | Hs.474751 | MYH9 | Myosin, heavy polypeptide 9, nonmuscle | 22q13.1 | 2 | 70 | 0.020 | ≤0.001 |
| TGCGAGACCA | Hs.490038 | CPA2 | Carboxypeptidase A2 (pancreatic) | 7q32 | 0 | 24 | 0.035 | ≤0.001 |
| CATTGCTTCT | Hs.516297 | TCF7L1 | Transcription factor 7‐like 1 (T‐cell specific, HMG‐box) | 2p11.2 | 0 | 82 | 0.010 | ≤0.001 |
| CAGTGTTCTT | Hs.518611 | TBC1D14 | TBC1 domain family, member 14 | 4p16.1 | 2 | 29 | 0.040 | ≤0.001 |
| AATGTACCAA | Hs.523130 | LIPF | Lipase, gastric | 10q23.31 | 1 | 51 | 0.010 | ≤0.001 |
| CAGTGCTTCT | Hs.527922 | DLEU1 | Deleted in lymphocytic leukemia, 1 | 13q14.3 | 349 | 8046 | 0.020 | ≤0.001 |
| ACCTCCCCAC | Hs.529117 | CYP2B7P1 | Cytochrome P450, family 2, subfamily B, polypeptide 7 pseudogene 1 | 19q13.2 | 1 | 41 | 0.010 | ≤0.001 |
| CAGTGCTTTT | Hs.551178 | Hs.551178 | CDNA FLJ46627 fis, clone TRACH2010272 | 1 | 60 | 0.010 | ≤0.001 | |
| GAGATTATGT | Hs.551521 | KCNE2 | Potassium voltage‐gated channel, Isk‐related family, member 2 | 21q22.12 | 5 | 55 | 0.050 | ≤0.001 |
| TGTACCTCAG | Hs.558365 | ORM2 | Orosomucoid 2 | 9q32 | 1 | 25 | 0.020 | ≤0.001 |
| TCATTCTGAA | Hs.69319 | GKN1 | Gastrokine 1 | 2p13.3 | 51 | 3592 | 0.010 | ≤0.001 |
| AATGTCCCCA | Hs.76253 | ATXN2 | Ataxin 2 | 12q24.1 | 2 | 37 | 0.030 | ≤0.001 |
| TTAACCCCTC | Hs.78224 | RNASE1 | Ribonuclease, RNase A family, 1 (pancreatic) | 14q11.2 | 26 | 219 | 0.070 | ≤0.001 |
T4, tag number in all tumor samples tested; N4, tag number in all normal samples. The expression of all genes was significantly altered in at least three tumor samples (P ≤ 0.05), as compared to all normal samples. At least two tumors showed more than fivefold change (P ≤ 0.01). Tags with “0” value were replaced with arbitrary 0.5 values for relative calculation of fold expression. The ratio was calculated after normalization to total tag numbers.