Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.

ABSTRACT: Given that the majority of multi-exon genes generate diverse functional products, it is important to evaluate expression at the isoform level. Previous studies have demonstrated strong gene-level correlations between RNA sequencing (RNA-seq) and microarray platforms, but have not studied their concordance at the isoform level. We performed transcript abundance estimation on raw RNA-seq and exon-array expression profiles available for common glioblastoma multiforme samples from The Cancer Genome Atlas using different analysis pipelines, and compared both the isoform- and gene-level expression estimates between programs and platforms. The results showed better concordance between RNA-seq/exon-array and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) platforms for fold

SUBMITTER: Dapas M 

PROVIDER: S-EPMC5444266 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature