IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
2011
IsoformEx: A New Method for Estimating Gene Expression from mRNA-Seq Data
publication
Evidence: high
Author Information
Author(s): Kim Hyunsoo, Bi Yingtao, Pal Sharmistha, Gupta Ravi, Davuluri Ramana V
Primary Institution: The Wistar Institute
Hypothesis
Can a novel algorithm accurately estimate transcript expression levels from mRNA-Seq data?
Conclusion
IsoformEx is a fast and accurate algorithm for estimating transcript expression levels, outperforming existing methods.
Supporting Evidence
- IsoformEx showed lower estimation errors and higher correlation coefficients compared to other methods.
- The algorithm was validated using both simulated and real mRNA-Seq data.
- IsoformEx accurately estimated expression levels in qRT-PCR experiments.
Takeaway
IsoformEx helps scientists understand how much of each gene is active by looking at tiny pieces of genetic material called transcripts.
Methodology
The study developed IsoformEx, which uses weighted non-negative least squares to estimate transcript expression levels from mRNA-Seq data.
Limitations
The algorithm assumes a transcript model is given and may not identify novel isoforms.
Digital Object Identifier (DOI)
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