In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants

BMC Genomics
Lenora W M LooLoic Le Marchand

Abstract

Genome-wide association studies have identified 55 genetic variants associated with colorectal cancer risk to date. However, potential causal genes and pathways regulated by these risk variants remain to be characterized. Therefore, we performed gene ontology enrichment and pathway analyses to determine if there was an enrichment of genes in proximity to the colorectal cancer risk variants that could further elucidate the probable causal genes and pathways involved in colorectal cancer biology. For the 65 unique genes that either contained, or were immediately neighboring up- and downstream, of these variants there was a significant enrichment for the KEGG pathway, Pathways in Cancer (p-value = 2.67 × 10-5) and an enrichment for multiple biological processes (FDR < 0.05), such as cell junction organization, tissue morphogenesis, regulation of SMAD protein phosphorylation, and odontogenesis identified through Gene Ontology analysis. To identify potential causal genes, we conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using gene expression and genotype data from the Genotype-Tissue Expression (GTEx) Project portal in normal sigmoid (n = 124) and transverse (n = 169) colon tissue. In addition, we also did a...Continue Reading

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Citations

Nov 27, 2018·Briefings in Bioinformatics·Quanhu ShengYan Guo
Jun 6, 2018·Frontiers in Genetics·Yili WuQihua Tan
Nov 18, 2017·Familial Cancer·Sanne W Ten BroekeMaartje Nielsen
Jan 29, 2021·Frontiers in Cell and Developmental Biology·Yu-Hang ZhangYu-Dong Cai
May 4, 2021·International Journal of Cancer. Journal International Du Cancer·Peter G Vaughan-ShawMalcolm G Dunlop

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Methods Mentioned

BETA
Phenotyping
immunoprecipitation
ChIP
ChIP seq
ChIP-Seq

Software Mentioned

HaploReg
Polymorphism Phenotyping ( PolyPhen -
JASPAR
PolyPhen2

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