Integrated genomic analysis-based identification of core pathways and driver genes associated with colorectal carcinoma
10.3724/SP.J.1008.2015.00619
- Author:
Hua MIAO
1
Author Information
1. Department of Surgery, The First People’s Hospital of Pinghu
- Publication Type:Journal Article
- Keywords:
Colorectal neoplasms;
Computational biology;
Core pathways;
Driver genes
- From:
Academic Journal of Second Military Medical University
2015;36(6):619-626
- CountryChina
- Language:Chinese
-
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 comoine tKe 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. Cf inder 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 subnetwork 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 77 genes including UBE2C and AURKA are the driver genes of the pathways.
