Introduction

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.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 higher correlation with known transcript expression levels from simulated mRNA-Seq data, and higher agreement with qRT-PCR measurements of specific transcripts for real mRNA-Seq data.IsoformEx is a fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. The software is available at http://bioinformatics.wistar.upenn.edu/isoformex.

Publications

  1. IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.
    Cite this
    Kim H, Bi Y, Pal S, Gupta R, Davuluri RV, 2011-07-01 - BMC bioinformatics

Credits

  1. Hyunsoo Kim
    Developer

    Center for Systems and Computational Biology, The Wistar Institute, United States of America

  2. Yingtao Bi
    Developer

  3. Sharmistha Pal
    Developer

  4. Ravi Gupta
    Developer

  5. Ramana V Davuluri
    Investigator

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Summary
AccessionBT000179
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByRamana V Davuluri