IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.

ABSTRACT:

Background

mRNA-Seq technology has revolutionized the field of transcriptomics for identification and quantification of gene transcripts not only at gene level but also at isoform level. Estimating the expression levels of transcript isoforms from mRNA-Seq data is a challenging problem due to the presence of constitutive exons.

Results

We propose a novel algorithm (IsoformEx) that employs weighted non-negative least squares estimation method to estimate the expression levels of transcript isoforms. Validations based on in silico simulation of mRNA-Seq and qRT-PCR experiments with real mRNA-Seq data showed that IsoformEx could accurately estimate transcript expression levels. In comparisons with published methods, the transcript expression levels estimated by IsoformEx showed

SUBMITTER: Kim H 

PROVIDER: S-EPMC3180389 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature