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