title: A generalized dSpliceType framework to detect differential splicing and differential expression events using RNA-Seq.
abstract: 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, we propose a generalized dSpliceType framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. We 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. We compared dSpliceType with two other methods in terms of five most common types of differential splicing events between two conditions using RNA-Seq. dSpliceType is free, available from http://dsplicetype.sourceforge.net/.
authors: Dongxiao
authors: D
authors: Zhu
authors: Nan
authors: N
authors: Deng
authors: Changxin
authors: C
authors: Bai
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D012326:RNA Splicing / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012333:RNA, Messenger