Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

ABSTRACT: High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the like

SUBMITTER: Zhang W 

PROVIDER: S-EPMC4689380 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature