title: Identification of key genes associated with colorectal cancer based on the transcriptional network.
abstract: Colorectal cancer (CRC) is among the most lethal human cancers, but the mechanism of the cancer is still unclear enough. We aimed to explore the key genes in CRC progression. The gene expression profile (GSE4183) of CRC was obtained from Gene Expression Omnibus database which included 8 normal samples, 15 adenoma samples, 15 CRC samples and 15 inflammatory bowel disease (IBD) samples. Thereinto, 8 normal, 15 adenoma, and 15 CRC samples were chosen for our research. The differentially expressed genes (DEGs) in normal vs. adenoma, normal vs. CRC, and adenoma vs. CRC, were identified using the Wilcoxon test method in R respectively. The interactive network of DEGs was constructed to select the significant modules using the Pearson's correlation. Meanwhile, transcriptional network of DEGs was also constructed using the g: Profiler. Totally, 2,741 DEGs in normal vs. adenoma, 1,484 DEGs in normal vs. CRC, and 396 DEGs in adenoma vs. CRC were identified. Moreover, function analysis of DEGs in each group showed FcR-mediated phagocytosis pathway in module 1, cardiac muscle contraction pathway in module 6, and Jak-STAT signaling pathway in module 19 were also enriched. Furthermore, MZF1 and AP2 were the transcription factor in module 6, with the target SP1, while SP1 was also a transcription in module 20. DEGs like NCF1, AKT, SP1, AP2, MZF1, and TPM might be used as specific biomarkers in CRC development. Therapy targeting on the functions of these key genes might provide novel perspective for CRC treatment.
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, China.
authors.forename: Guoting
authors.initials: G
authors.lastname: Chen
authors.forename: Hengping
authors.initials: H
authors.lastname: Li
authors.forename: Xianping
authors.initials: X
authors.lastname: Niu
authors.forename: Guofeng
authors.initials: G
authors.lastname: Li
authors.forename: Ning
authors.initials: N
authors.lastname: Han
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Guang
authors.initials: G
authors.lastname: Li
authors.forename: Yangzhou
authors.initials: Y
authors.lastname: Liu
authors.forename: Guixin
authors.initials: G
authors.lastname: Sun
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Zengchun
authors.initials: Z
authors.lastname: Li
authors.forename: Qinchuan
authors.initials: Q
authors.lastname: Li
mesh_terms: D000236:Adenoma / Q000235:genetics*; D014408:Biomarkers, Tumor / Q000235:genetics*; D003106:Colon / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000235:genetics*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D012007:Rectum / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D014157:Transcription Factors