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. 2014 May 29;9(5):e98293. doi: 10.1371/journal.pone.0098293

Table 1. Identification of cancer amplified genes with high copy number versus expression correlation.

Gene name Entrez ID Chr r Description
NSD3/WHSC1L1 54904 8 0.68 Histone methyltransferase
SETDB1 9869 1 0.64 Histone methyltransferase
PPFIA1 8500 11 0.62 LAR protein-tyrosine phosphatase-interacting protein (liprin)
FRS2 10818 12 0.62 Adapter protein (FGFR/MAPK signaling)
APH1A 51107 1 0.6 Gamma-secretase complex subunit (Notch pathway)
ERCC5 2073 13 0.6 DNA endonuclease (DNA excision repair)
FADD 8772 11 0.58 Apoptotic adaptor, candidate driver oncogene
YEATS4 8089 12 0.57 NuA4 histone acetyltransferase (HAT) complex subunit
MDM2 4193 12 0.56 E3 ubiquitin-protein ligase linked to p53
KRAS 3845 12 0.56 GTPase, proto-oncogene
GTPBP4 23560 10 0.55 GTPase, negative regulator of p53
IKBKB 3551 8 0.54 Serine kinase (NF-KB pathway)
DCUN1D1 54165 3 0.53 E3 ubiquitin ligase complex subunit, candidate oncogenic driver
RAD52 5893 12 0.53 DNA damage repair enzyme
CHD1L 9557 1 0.52 DNA helicase involved in DNA damage response
ARNT 405 1 0.51 HIF1 complex subunit
PRPF6 24148 20 0.51 Spliceosome component (U4/U6-U5 tri-snRNP complex)
PRKCI 5584 3 0.5 Serine/threonine kinase (NF-KB pathway)
BCL9 607 1 0.48 Trancriptional regulator linked to Wnt signaling
EGFR 1956 7 0.48 Receptor tyrosine kinase
RAD51AP1 10635 12 0.48 DNA damage response/repair gene
NOTCH2 4853 1 0.47 Type 1 transmembrane protein (Notch pathway)
NDUFC2 4718 11 0.47 NADH dehydrogenase (Complex I) accessory subunit
GRB7 2886 17 0.47 Adapter protein (EGFR/MAPK pathway)
ERC1 23085 12 0.46 Regulatory subunit of IKK complex (NF-KB pathway)
RAP1B 5908 12 0.46 GTPase, Ras oncogene family
ERBB2 2064 17 0.45 Receptor tyrosine kinase
BRD4 23476 19 0.45 Epigenetic regulatory gene, chromatin reader
MDM4 4194 1 0.44 Nuclear protein, negative regulator of p53
PIAS3 10401 1 0.42 Small ubiquitin-like modifier (SUMO) ligase (JAK/STAT)
PRKAB2 5565 1 0.42 AMP-activated protein kinase (AMPK) subunit
CCNE1 898 19 0.41 Cell cycle regulator (G1-S)
TPX2 22974 20 0.41 Spindle assembly factor, linked to Aurka
PIK3CA 5290 3 0.4 Phosphoinositide-3-kinase (PI3K) subunit
CCND3 896 6 0.4 Cell cycle regulator (G1-S)
WNK1 65125 12 0.4 Serine/threonine kinase, mitotic kinase
RTEL1 51750 20 0.37 ATP-dependent DNA helicase (DNA repair)
IGF1R 3480 15 0.36 Receptor tyrosine kinase
FGFR3 2261 4 0.3 Receptor tyrosine kinase
CDK6 1021 7 0.3 Serine/threonine-protein kinase, cell cycle regulator