RPASE: Individual‐based allele‐specific expression detection without prior knowledge of haplotype phase. (20th June 2018)

• Record Type: Journal Article
• Authors: Wang, Mi; Uebbing, Severin; Pawitan, Yudi; Scofield, Douglas G.
• Is Part Of: Molecular ecology resources. Volume 18:Number 6(2018:Nov.)
• Page Start: 1247
• Page End: 1262
• Publication Date: 2018-06-20
• Subjects: allele‐specific expression -- gene expression evolution -- regulatory variation -- RNA‐seq; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12909
• Languages: English
• ISSNs: 1755-098X

Abstract

Abstract: Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele‐specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read‐backed Phasing‐based ASE detection) to test for genes that show ASE. With mapped RNA‐seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual‐based gene‐level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.