ArticleBMC bioinformatics2011
IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Transcriptome-Wide Association Analysis of Flavonoid Biosynthesis Genes and Their Correlation With Leaf Phenotypes in Hawk Tea (Ecology and evolution · 2024Article
- EV-origin: Enumerating the tissue-cellular origin of circulating extracellular vesicles using exLR profile.Computational and structural biotechnology journal · 2020Article
- A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance.Molecular cancer research : MCR · 2019Article
- Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.Nature communications · 2017Article
- Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.Briefings in bioinformatics · 2017Article
- Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.BMC bioinformatics · 2015Article
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- RNA-Seq technology and its application in fish transcriptomics.Omics : a journal of integrative biology · 2014Review
- RNA-Seq gene profiling--a systematic empirical comparison.PloS one · 2014Article
- CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation.Nucleic acids research · 2014Article
- NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.BMC bioinformatics · 2013Article
- High-throughput sequencing of cytosine methylation in plant DNA.Plant methods · 2013Article
- Simultaneous isoform discovery and quantification from RNA-seq.Statistics in biosciences · 2013Article
- Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.PLoS computational biology · 2013Article
- DBATE: database of alternative transcripts expression.Database : the journal of biological databases and curation · 2013Article
- Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Frontiers in plant science · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundmRNA-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.
resultsWe 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.
conclusionsIsoformEx 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.
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