dSpliceType – A Generalized Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq

Transcriptomes are routinely compared in term of a list of differentially expressed genes followed by functional enrichment analysis. Due to the technology limitations of microarray, the molecular mechanisms of differential expression is poorly understood. Using RNA-seq data, researchers at Wayne State University propose a generalized dSpliceType framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. They applied the method to two public RNA-seq data sets and compared the transcriptomes between treatment and control conditions. The generalized dSpliceType detects and prioritizes a list of genes that are differentially expressed and/or spliced. In particular, the multivariate dSpliceType is among the fist to utilize sequential dependency of normalized base-wise read coverage signals and capture biological variability among replicates using a multivariate statistical model. The researchers compared dSpliceType with two other methods in terms of five most common types of differential splicing events between two conditions using RNA-Seq.

rna-seq

Availability – dSpliceType is free available from http://dsplicetype.sourceforge.net/

Zhu D, Deng N, Bai C. (2015) A Generalized dSpliceType Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq. IEEE Trans Nanobioscience [Epub ahead of print]. [abstract]

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