TY  - JOUR
N1  - Open Access
ID  - open2339
UR  - https://www.mdpi.com/1422-0067/20/14/3582
IS  - 14
A1  - Kumar, Rajesh
A1  - Patiyal, Sumeet
A1  - Kumar, Vinod
A1  - Nagpal, Gandharva
A1  - Raghava, G.P.S.
Y1  - 2019/07/22/
N2  - 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.
PB  - MDPI (Basel, Switzerland)
JF  - International journal of molecular sciences
VL  - 20
KW  - adenocarcinoma; copy number variation; differential expressed genes; enhancer; functional enrichment analysis; pancreatic cancer; regulatory elements; super enhancer; survival
SN  - 1422-0067
TI  - In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma.
ER  -