Integrated genomic analysis-based identification of core pathways and driver genes associated with colorectal carcinoma
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The First People’s Hospital of Pinghu,Zhejiang Pinghu,Department of Colorectal Surgery,Changhai Hospital,Second Military Medical University,Department of Colorectal Surgery,Changhai Hospital,Second Military Medical University,The First People’s Hospital of Pinghu,Zhejiang Pinghu,The First People’s Hospital of Pinghu,Zhejiang Pinghu,Department of Colorectal Surgery,Changhai Hospital,Second Military Medical University,Department of Colorectal Surgery,Changhai Hospital,Second Military Medical University

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    Abstract:

    Objective To investigate the core pathways and driver genes associated with development of colorectal carcinoma (CRC). Methods Meta-analysis was employed to screen differently expressed genes between CRC and the adjacent normal mucosa in 5 studies. ComBat was used to combine the gene data of the 5 studies and then the differently expressed genes were used to construct a stable co-expression network in CRC using PCIT software. CFinder software was used to extract the core sub-networks of the constructed coexpression network, and Gather software was used for functional enrichment analysis of the core subnetworks. Finally, those genes with up-regulation and DNA gain in CRC or down-regulation and DNA loss were identified as driver genes. Results Our meta-analysis found 2 073 differently expressed genes between CRC and the adjacent normal mucosa, including 1 174 up-regulated and 899 down-regulated in 5 the CRC studies. A coexpression network was constructed with those differently expressed genes; it had 798 nodes, 1 462 edges, and 22 core subnetworks. The largest sub-network consisted 77 genes and 436 edges, and the function mainly involved cell cycle and proliferation regulation, with the driver genes including UBE2C, MYBL2, FAM83D, AURKA and TPX2. Conclusion Cell cycle and proliferation pathways are the core ones in the development of CRC, and 11 genes including UBE2C and AURKA are the driver genes of the pathways.

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History
  • Received:December 13,2014
  • Revised:April 28,2015
  • Adopted:June 03,2015
  • Online: June 23,2015
  • Published:
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