title: 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 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104-4268, USA.
authors.forename: Hyunsoo
authors.initials: H
authors.lastname: Kim
authors.forename: Yingtao
authors.initials: Y
authors.lastname: Bi
authors.forename: Sharmistha
authors.initials: S
authors.lastname: Pal
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016018:Least-Squares Analysis; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger