TISA: tissue-specific alternative splicing in human and mouse genes

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Title
TISA: tissue-specific alternative splicing in human and mouse genes
Author(s)
Seung Jae Noh; Kyooyeol Lee; Hyojung Paik; Cheol-Goo Hur
Bibliographic Citation
DNA Research, vol. 13, no. 5, pp. 229-243
Publication Year
2006
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/).
Keyword
alternative splicinggene ontologygenome-based clusteringsplice graphtissue-specifictranscript variants
ISSN
1340-2838
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/dnares/dsl011
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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