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In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma.
 
Creator Kumar, Rajesh
Patiyal, Sumeet
Kumar, Vinod
Nagpal, Gandharva
Raghava, G.P.S.
 
Subject QR Microbiology
 
Description Understanding the gene regulatory network governing cancer initiation and progression is necessary, although it remains largely unexplored. Enhancer elements represent the center of this regulatory circuit. The study aims to identify the gene expression change driven by copy number variation in enhancer elements of pancreatic adenocarcinoma (PAAD). The pancreatic tissue specific enhancer and target gene data were taken from EnhancerAtlas. The gene expression and copy number data were taken from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) and copy number variations (CNVs) were identified between matched tumor-normal samples of PAAD. Significant CNVs were matched onto enhancer coordinates by using genomic intersection functionality from BEDTools. By combining the gene expression and CNV data, we identified 169 genes whose expression shows a positive correlation with the CNV of enhancers. We further identified 16 genes which are regulated by a super enhancer and 15 genes which have high prognostic potential (-score > 1.96). Cox proportional hazard analysis of these genes indicates that these are better predictors of survival. Taken together, our integrative analytical approach identifies enhancer CNV-driven gene expression change in PAAD, which could lead to better understanding of PAAD pathogenesis and to the design of enhancer-based cancer treatment strategies.
 
Publisher MDPI (Basel, Switzerland)
 
Date 2019-07-22
 
Type Article
PeerReviewed
 
Relation https://www.mdpi.com/1422-0067/20/14/3582
http://crdd.osdd.net/open/2339/
 
Identifier Kumar, Rajesh and Patiyal, Sumeet and Kumar, Vinod and Nagpal, Gandharva and Raghava, G.P.S. (2019) In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. International journal of molecular sciences, 20 (14). ISSN 1422-0067