Table 1.

Pearson's correlations of array CGH and expression for each gene in the analysis (i.e., self-self comparisons)

Cytogenetic locationSymbolGene namecDNA expression array
Oligonucleotide expression array
R*PQRPQ
1p36.13EPHA2Ephrin receptor EphA2−0.010.991.00−0.070.991.00
1p31.2GADD45AGrowth arrest- and DNA damage–inducible gene GADD45, α0.560.040.020.460.030.01
1p13.3CSF1Colony-stimulating factor 1 (macrophage)0.180.840.660.090.981.00
1q23.3DDR2Discoidin domain receptor family, member 20.150.900.890.110.981.00
1q32.1ELF3E74-like factor 3 (ets domain transcription factor, epithelial specific)0.330.460.140.270.530.20
2p21MSH2mutS homologue 2, colon cancer, nonpolyposis type 1 (Escherichia coli)0.190.840.560.170.900.64
2q23.3ARHEras homologue gene family, member E0.210.840.490.170.900.64
2q24.1ACVR1activin A receptor, type I0.220.810.430.090.981.00
3p25.3VHLvon Hippel-Lindau syndrome0.320.460.140.290.460.17
3p25.2RAF1v-raf-1 murine leukemia viral oncogene homologue 10.610.020.020.410.070.03
3p21.31CDC25ACell division cycle 25A0.590.030.020.340.250.08
3p21.31ARHAras homologue gene family, member A0.610.020.020.340.250.08
3p21.1TKTTransketolase (Wernicke-Korsakoff syndrome)0.320.470.150.240.650.28
3q12.1DOC1Down-regulated in ovarian cancer 1−0.280.991.00−0.140.991.00
3q23PLS1Plastin 1 (I isoform)−0.250.991.00−0.060.991.00
3q24AGTR1Angiotensin II receptor, type 10.250.720.32−0.020.991.00
3q27.3BCL6B-cell CLL/lymphoma 6 (zinc finger protein 51)0.280.610.230.160.910.73
3q29TFRCTransferrin receptor (p90, CD71)0.350.400.110.480.030.01
4p16.3FGFR3Fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism)0.330.460.140.380.120.04
4q12PDGFRAPlatelet-derived growth factor receptor, α polypeptide0.490.100.030.350.220.07
4q27CCNA2Cyclin A20.630.020.020.510.020.01
5q13.2CCNB1Cyclin B10.370.340.090.340.260.08
5q31.2CDC25CCell division cycle 25C0.290.570.200.310.330.11
6p21.31CDKN1ACyclin-dependent kinase inhibitor 1A (p21, Cip1)−0.030.991.000.10.981.00
6p21.2PIM1Proto-oncogene serine/threonine-protein kinase pim-1 (ec 2.7.1.37)0.360.390.110.270.480.18
6q21FYNFYN tyrosine kinase proto-oncogene0.110.951.000.120.981.00
8p12FGFR1Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome)0.330.460.140.310.330.11
8q12.1LYNv-yes-1 Yamaguchi sarcoma viral related oncogene homologue0.260.690.280.380.110.04
8q12.1RAB2RAB2, member RAS oncogene family0.260.690.280.230.730.34
9q31.3GNG10Guanine nucleotide binding protein (G protein), γ 100.20.840.510.20.860.51
10p12.2BMIMurine leukemia viral (bmi-1) oncogene homologue0.260.690.290.070.981.00
11p15.4ARHGras homologue gene family, member G (ρ G)0.330.460.140.340.230.08
11q13.1MEN1Multiple endocrine neoplasia I0.440.180.05−0.050.991.00
11q13.3CCND1Cyclin D1 (PRAD1: parathyroid adenomatosis 1)0.430.190.050.450.040.01
11q13.3EMS1Src substrate cortactin (amplaxin; oncogene ems1)0.570.040.020.40.080.03
11q13.5PAK1p21/Cdc42/Rac1-activated kinase 1 (STE20 homologue, yeast)0.010.991.000.040.981.00
11q14.2CTSCCathepsin C0.230.790.400.220.770.39
11q21MRE11AMRE11 meiotic recombination 11 homologue A (Saccharomyces cerevisiae)0.630.020.020.340.250.08
12q14.1SASSarcoma-amplified sequence0.180.840.640.00190.991.00
12q23.3TRA1Tumor rejection antigen (gp96) 10.280.620.230.150.910.76
12q24.12ALDH2Aldehyde dehydrogenase 2 family (mitochondrial)0.080.971.000.110.981.00
12q23.3TDGThymine-DNA glycosylase0.330.460.140.240.630.26
14q11.2APEXAPEX nuclease (multifunctional DNA repair enzyme) 10.580.040.020.30.370.13
14q11.2PSME1Proteasome (prosome, macropain) activator subunit 1 (PA28 α)0.060.981.000.270.500.19
14q32.33AKT1v-akt murine thymoma viral oncogene homologue 10.420.200.050.360.170.06
15q24.1PMLacute promyelocytic leukemia, inducer−0.040.991.000.170.900.64
15q24.1CSKc-src tyrosine kinase0.510.080.020.280.460.17
16q22.1CDH1Cadherin 1, type 1, E-cadherin (epithelial)−0.010.991.00−0.030.991.00
17q12ERBB2v-erb-b2 avian erythroblastic leukemia viral oncogene homologue 20.460.130.040.50.020.01
17q21.2TOP2ATopoisomerase (DNA) II α, 170 kDa0.440.170.050.310.330.11
18p11.23PTPRMProtein tyrosine phosphatase, receptor type, M0.220.810.430.110.981.00
19p13.2JUNBJun B proto-oncogene0.190.840.560.20.870.54
19q13.33LIG1Ligase I, DNA, ATP dependent0.320.460.140.10.981.00
20p13FKBP1AFK506 binding protein 1A, 12 kDa0.490.090.030.530.010.01
20p13CDC25BCell division cycle 25B0.310.510.170.280.480.17
20p11.23SEC23BSec23 homologue B (S. cerevisiae)0.530.060.020.490.020.01
20q13.12MYBL2v-myb myeloblastosis viral oncogene homologue (avian)-like 20.220.810.430.190.880.59
20q13.12PRKCBP1protein kinase C binding protein 10.20.840.540.240.690.31
20q13.13CSE1LCSE1 chromosome segregation 1-like (yeast)0.580.040.020.440.050.02
20q13.13PTPN1Protein tyrosine phosphatase, non-receptor type 1−0.030.991.000.180.900.64
21q22.3MX2Myxovirus (influenza virus) resistance 2 (mouse)0.380.320.090.050.981.00
21q22.3SMT3H1SMT3 suppressor of mif two 3 homologue 3 (yeast)0.430.190.050.410.070.03
22q13.1ATF4Activating transcription factor 4 (tax-responsive enhancer element B67)0.050.981.000.280.480.17
Xq23§PRKCIProtein kinase C, iota−0.010.991.00−0.110.991.00
  • * Pearson's correlation coefficient.

  • Westfall-Young P for finding a correlation for any gene as big as the observed correlation under the null hypothesis of zero correlation (27).

  • Benjamini-Hochberg procedure Q representing the smallest false discovery rate for declaring the gene positively correlated (28).

  • § Reassigned in July 2003 to 3q26.2.