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Table 4 Comparison of gene expression in copy number loss/gain genes with LOH and without LOH*

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 with LOH Fold change without LOH T-test P-value
Table 4.a.: Genes/probes with CN loss (CN = 1)
ATXN7 chr3p21.1-p12 204516_at 4 2 10 0.574 0.258 -8.233 1.333E-03
CTDSPL chr3p21.3 213597_s_at 3 3 13 0.997 0.890 -5.414 8.188E-03
F2R chr5q13 203989_x_at 3 2 4 6.083 1.217 -6.771 7.275E-03
RAB5A chr3p24-p22 209089_at 5 2 6 0.419 0.240 -9.065 5.698E-04
RAF1 chr3p25 201244_s_at 3 2 9 0.555 0.389 -24.008 5.074E-04
SCN10A chr3p22-p21 208578_at 3 4 23 1.806 0.884 -4.253 8.107E-03
Table 4.b.: Genes/probes with CN gain (CN = 3 or 4)
ARHGAP5 chr14q12 217936_at 2 5 1 1.731 0.769 -4.809 8.159E-03
CYP11B1 chr8q21 214610_at 2 6 3 0.915 1.114 4.728 3.469E-03
NFATC4 chr14q11.2 205897_at 2 3 1 1.363 0.903 -11.692 2.823E-03
PAX9 chr14q12-q13 207059_at 2 5 1 0.898 0.319 -5.395 5.706E-03
PPFIA1 chr11q13.3 202066_at 7 2 12 7.524 2.448 -3.918 6.425E-03
TP63 chr3q28 211834_s_at 2 13 17 0.901 1.197 3.438 9.809E-03
TP63 chr3q28 211194_s_at 2 13 18 0.987 2.649 4.008 3.640E-03
  1. *Sorted alphabetically by gene name