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Table 3 Comparison of gene expression in copy number neutral (CNN) genes with LOH and without LOH (normal) (N = 46 genes significantly differentially-expressed 2-fold or greater)*

From: Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma

Gene name Cytoband Probeset on U133A array No. cases with LOH No. cases without LOH No. SNPs Fold change CNN with LOH Fold change CNN without LOH T-test P-value
Genes where expression level of CNN with LOH is less than CNN without LOH (N = 28 genes)
ADK chr10q22|10q11-q24 204120_s_at 2 13 46 0.404 0.606 3.138 8.559E-03
ADK chr10q22|10q11-q24 204119_s_at 2 13 46 0.411 0.619 3.195 7.278E-03
AIM1L chr1p36.11 220289_s_at 2 15 6 0.093 0.201 3.548 4.812E-03
APOL6 chr22q12.3 219716_at 2 5 4 0.467 0.894 4.659 9.543E-03
ATP6V0E1 chr5q35.2 201171_at 2 12 5 0.375 0.669 3.234 9.843E-03
ATP6V0E1 chr5q35.2 200096_s_at 2 12 5 0.480 0.872 4.445 5.699E-03
BACH1 chr21q22.11 204194_at 2 12 9 0.498 0.738 3.970 2.098E-03
BTG2 chr1q32 201236_s_at 2 14 1 0.460 0.986 4.095 1.183E-03
CD2 chr1p13.1 205831_at 2 14 1 0.324 0.628 3.462 9.221E-03
CEACAM6 chr19q13.2 211657_at 2 13 3 0.007 0.100 4.779 7.023E-03
CRAT chr9q34.1 209522_s_at 7 8 1 0.293 0.567 3.169 7.495E-03
CSDE1 chr1p22 202646_s_at 2 14 3 0.343 0.895 7.835 7.590E-05
CYP4F3 chr19p13.2 206515_at 2 13 136 0.065 0.307 3.329 5.631E-03
DIO2 chr14q24.2-q24.3 203699_s_at 2 11 4 0.072 0.127 3.565 6.175E-03
DIO2 chr14q24.2-q24.3 203700_s_at 2 11 4 0.168 0.280 3.697 3.752E-03
EIF4EBP2 chr10q21-q22 208770_s_at 2 14 1 0.452 0.657 6.300 2.692E-05
FAS chr10q24.1 216252_x_at 2 13 8 0.412 0.648 3.058 9.883E-03
HERC6 chr4q22.1 219352_at 3 9 1 0.105 0.538 5.769 2.901E-04
ICAM3 chr19p13.3-p13.2 204949_at 2 13 2 0.356 0.602 3.478 4.342E-03
IL1RN chr2q14.2 212659_s_at 2 12 13 0.073 0.142 3.256 7.793E-03
NADSYN1 chr11q13.4 218840_s_at 2 8 10 0.448 0.649 3.399 9.384E-03
NHP2 chr5q35.3 216583_x_at 2 10 1 0.497 0.774 4.091 2.584E-03
PDCD4 chr10q24 202730_s_at 2 12 4 0.212 0.363 4.483 9.256E-04
PPP1R13L chr19q13.32 218849_s_at 3 13 1 0.190 0.487 5.016 5.018E-04
RIPK4 chr21q22.3 221215_s_at 5 10 7 0.217 0.454 3.614 3.658E-03
SKAP2 chr7p21-p15 216899_s_at 2 10 12 0.293 0.615 4.165 1.973E-03
SKAP2 chr7p21-p15 204361_s_at 2 10 43 0.359 0.665 4.384 1.591E-03
SLC6A1 chr3p25-p24 205152_at 2 8 6 0.158 0.438 5.044 2.481E-03
STK39 chr2q24.3 202786_at 2 12 86 0.151 0.290 3.363 6.327E-03
SYNPO2L chr10q22.2 219804_at 3 13 1 0.063 0.345 6.925 8.703E-06
TGM5 chr15q15.2 207911_s_at 2 13 8 0.382 0.517 3.496 4.389E-03
ZNF91 chr19p13.1-p12 206059_at 2 10 5 0.026 0.551 9.054 6.430E-04
Genes where expression level of CNN with LOH is greater than CNN without LOH (N = 18 genes)
ACVR1 chr2q23-q24 203935_at 2 12 13 3.480 1.751 -4.533 7.869E-04
ASPN chr9q22 219087_at 5 10 2 10.594 2.679 -3.792 2.667E-03
BUB1 chr2q14 209642_at 2 12 2 8.571 4.010 -3.922 2.170E-03
CALU chr7q32.1 200757_s_at 2 12 7 3.467 1.830 -4.612 7.505E-04
CALU chr7q32.1 200755_s_at 2 12 7 3.899 1.981 -3.903 2.269E-03
CAMSAP1L1 chr1q32.1 212765_at 2 13 3 3.000 1.357 -6.288 1.629E-03
CENPF chr1q32-q41 209172_s_at 2 14 10 5.481 2.643 -5.909 3.926E-05
CSNK1E chr22q13.1 202332_at 2 3 4 2.933 1.157 -7.434 9.278E-03
FAM13A chr4q22.1 202973_x_at 3 10 14 2.756 1.149 -3.508 6.115E-03
FHL2 chr2q12-q14 202949_s_at 2 14 15 3.159 1.244 -4.697 4.097E-04
GSR chr8p21.1 205770_at 3 10 8 2.505 1.222 -3.701 4.824E-03
ITGA6 chr2q31.1 201656_at 2 11 21 4.038 2.400 -3.519 4.820E-03
KIF14 chr1q32.1 206364_at 2 13 6 11.027 3.578 -8.257 2.071E-06
NCAPH chr2q11.2 212949_at 2 11 2 3.643 1.943 -5.087 4.450E-04
NRP2 chr2q33.3 214632_at 3 11 29 2.161 1.257 -3.500 9.276E-03
RBM28 chr7q32.1 218593_at 2 11 9 2.210 1.555 -3.976 2.370E-03
SMAD5 chr5q31 205187_at 2 12 3 2.208 0.829 -10.692 3.171E-07
STEAP3 chr2q14.2 218424_s_at 2 14 12 2.707 1.207 -6.922 9.985E-06
TGS1 chr8q11 219231_at 2 8 1 2.533 1.656 -3.495 8.601E-03
  1. *Sorted alphabetically by gene name