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.
Bibliographical noteFunding Information:
We thank Ms. Julie Wilhelmy and Dr. Michael Mindrinos for help on RT-PCR experiments. This work was supported by the National Research Foundation of Korea (NRF) funded by the Korea government (No. NRF-2014R1A1A2A16050527). It was also funded by the Korea University Grant, NIH (U54-GM62119, P01-HG00205, R01-GM101401) and Shriners Research Grant (85500-BOS).
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