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. 2011 Aug 2;6(8):e22961. doi: 10.1371/journal.pone.0022961

Table 4. P values of the selective ten out of twenty seven pathways and gene sets with enrichment of genes with copy number losses (the complete twenty-seven gene sets are listed in Table S4).

MSigDB ID of gene set: brief description Blood Non-involved lung Discovery set Validation set Early stage tumors Late stage tumors All tumors
1 AGUIRRE_PANCREAS_CHR9: Genes on chromosome 9 with copy-number-driven expression in pancreatic adenocarcinoma. 0.25 0.57 <5×10−5 5×10−5 <5×10−5 <5×10−5 <5×10−5
2 HSA04080_NEUROACTIVE_LIGAND _RECEPTOR_INTERACTION: Genes involved in neuroactive ligand-receptor interaction 0.061 0.00050 0.00070 <5×10−5 <5×10−5 0.0042 5×10−5
3 CELL_CELL_SIGNALING: Genes annotated by the GO term GO:0007267. Any process that mediates the transfer of information from one cell to another. 0.80 0.061 0.0015 0.013 0.0017 0.0030 0.00070
4 HSA04140_REGULATION_OF_AUTOPHAGY: Genes involved in regulation of autophagy 0.16 <5×10−5 0.00065 0.0046 0.00095 0.00010 0.00085
5 SIGNAL_TRANSDUCTION: Genes involved in signal transduction 0.21 0.23 0.012 0.0019 0.011 0.022 0.0015
6 CELL_SURFACE_RECEPTOR_LINKED_SIGNAL_TRANSDUCTION_GO_0007166: Genes annotated by the GO term GO:0007166. Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell. 0.35 0.034 0.021 0.0017 0.027 0.00075 0.0031
7 CELL_CELL_ADHESION: Genes annotated by the GO term GO:0016337. The attachment of one cell to another cell via adhesion molecules. 0.53 0.069 0.0071 0.0085 0.0028 0.00035 0.0039
8 HDACI_COLON_CUR24HRS_DN: Downregulated by curcumin at 24 hrs in SW260 colon carcinoma cells 0.92 <5×10−5 0.0070 0.0020 0.0094 0.037 0.0050
9 REGULATION_OF_MITOTIC_CELL_CYCLE: Genes annotated by the GO term GO:0007346. Any process that modulates the rate or extent of progress through the mitotic cell cycle. 0.64 <5×10−5 0.0010 0.049 0.0075 0.017 0.0053
10 CHROMATIN_MODIFICATION: Genes annotated by the GO term GO:0016568. The alteration of DNA or protein in chromatin, which may result in changing the chromatin structure. 0.98 0.71 0.019 0.022 0.049 0.0095 0.021