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DNA Research Advance Access published online on November 14, 2006
DNA Research, doi:10.1093/dnares/dsl011
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© The Author 2006. Kazusa DNA Research Institute.
Received July 5, 2006
Revised October 15, 2006

Full Papers

TISA: Tissue-specific Alternative Splicing in Human and Mouse Genes

Seung-Jae Noh 1, Kyooyeol Lee 1, Hyojung Paik 1, and Cheol-Goo Hur 1 *

1 Bioinformatics Lab. Plant genomics center, KRIBB, 52 Eoeun-dong, Yuseong-gu, Daejon, 305-333 Korea

* To whom correspondence should be addressed.
Cheol-Goo Hur, E-mail: hurlee{at}kribb.re.kr


  Abstract

Alternative splicing (AS) is a mechanism by which multiple transcripts are produced from a single gene and is thought to be an important mechanism for tissue-specific expression of transcript isoforms. Here, we report a novel graphing method for transcript reconstruction and statistical prediction of tissue-specific AS. We applied three selection steps to generate the splice graph and predict the transcript isoforms: (i) a custom scoring rule for exon/intron sets, (ii) binomial statistics for selecting valid alternative splicing with a frequency of at least 1% for the predominant form and (iii) evaluation of transcript structure. We obtained 97 286 and 66 022 valid transcripts from 26 143 human and 27 741 mouse genes, respectively. In addition, we discovered 33 481 AS events for nine types of AS patterns in human. The statistical significance of tissue specificity for each gene, transcript and AS event was assessed based on EST tissue information, followed by a multiple testing correction procedure. In human, 12 711 genes, 16 016 transcripts and 1035 AS events were predicted to be tissue-specific (false discovery rate <0.01). This information on genes, transcript structures, AS events and their tissue specificities in human and mouse are freely accessible on the TISA website (http://tisa.kribb.re.kr/AGC/).

Keywords: alternative splicing; genome-based clustering; splice graph; transcript variants; tissue-specific; gene ontology.
Communicated by Kenta Nakai
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[Abstract] [Full Text] [PDF]


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