Platform-integrated mRNA isoform quantification [journal]

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Journal

Bioinformatics - April 15, 2020

Authors

Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang (associate professor), Wei Zhang

Abstract

Accurate estimation of transcript isoform abundance is critical for downstream transcriptome analyses and can lead to precise molecular mechanisms for understanding complex human diseases, like cancer. Simplex mRNA Sequencing (RNA-Seq) based isoform quantification approaches are facing the challenges of inherent sampling bias and unidentifiable read origins. A large-scale experiment shows that the consistency between RNA-Seq and other mRNA quantification platforms is relatively low at the isoform level compared to the gene level. In this project, we developed a platform-integrated model for transcript quantification (IntMTQ) to improve the performance of RNA-Seq on isoform expression estimation. IntMTQ, which benefits from the mRNA expressions reported by the other platforms, provides more precise RNA-Seq-based isoform quantification and leads to more accurate molecular signatures for disease phenotype prediction.

Link to full paper

Platform-integrated mRNA isoform quantification

Keywords

bioinformatics, computational biology