Identification of differentially expressed genes and their upstream regulators in colorectal cancer

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Abstract

To identify the differentially expressed genes (DEGs) and their transcription factors (TFs) in colorectal cancer (CRC). We performed an integrated analysis of microarray studies. Functional annotation and CRC-specific transcriptional regulatory network construction were performed. Expression of selected DEGs and TFs was verified with The Cancer Genome Atlas (TCGA) data sets and qRT-PCR. SurvMicro was used to analyze the correlation between the overall survival time of CRC patients and the expression of DEGs and TFs. Seven data sets were obtained and 2014 DEGs in CRC were identified. Pathways in cancer and fatty acid metabolism were significantly enriched pathways of upregulated and downregulated DEGs, respectively. Expression of five DEGs (RERGL, ESM1, CA1, ANGPTL7 and TMEFF2) and their five TFs (ZNF354C, ARID3A, NFIC, BRCA1 and ZEB1) was verified by TCGA data sets and qRT-PCR. Their expression in TCGA data sets was same as that in our integrated analysis. Only the expression of EMS1, NFIC, BRCA1 and ZEB1 was inconsistent with integrated analysis and TCGA data sets. Expression of RERGL and BRCA1 was significantly correlated with the overall survival time of CRC patients. These five DEGs may have roles in CRC regulated by their five upstream TFs, which may make a contribution in uncovering the mechanism and providing new strategy of diagnosis and therapies for CRC.

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