RASA: Robust alternative splicing analysis for human transcriptome arrays

Junhee Seok, Weihong Xu, Ronald W. Davis, Wenzhong Xiao

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Human transcriptome arrays (HTA) have recently been developed for high-throughput alternative splicing analysis by measuring signals not only from exons but also from exon-exon junctions. Effective use of these rich signals requires the development of computational methods for better gene and alternative splicing analyses. In this work, we introduce a computational method, Robust Alternative Splicing Analysis (RASA), for the analysis of the new transcriptome arrays by effective integration of the exon and junction signals. To increase robustness, RASA calculates the expression of each gene by selecting exons classified as not alternatively spliced. It then identifies alternatively spliced exons that are supported by both exon and junction signals to reduce the false positives. Finally, it detects additional alternative splicing candidates that are supported by only exon signals because the signals from the corresponding junctions are not well detected. RASA was demonstrated with Affymetrix HTAs and its performance was evaluated with mRNA-Seq and RT-PCR. The validation rate is 52.4%, which is a 60% increase when compared with previous methods that do not use selected exons for gene expression calculation and junction signals for splicing detection. These results suggest that RASA significantly improves alternative splicing analyses on HTA platforms.

Original languageEnglish
Article number11917
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 2015 Jul 6

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Alternative Splicing
Gene Expression Profiling
Exons
Transcriptome
Gene Expression
Polymerase Chain Reaction
Messenger RNA

ASJC Scopus subject areas

  • General

Cite this

RASA : Robust alternative splicing analysis for human transcriptome arrays. / Seok, Junhee; Xu, Weihong; Davis, Ronald W.; Xiao, Wenzhong.

In: Scientific Reports, Vol. 5, 11917, 06.07.2015.

Research output: Contribution to journalArticle

Seok, Junhee ; Xu, Weihong ; Davis, Ronald W. ; Xiao, Wenzhong. / RASA : Robust alternative splicing analysis for human transcriptome arrays. In: Scientific Reports. 2015 ; Vol. 5.
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