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Deducing Isoform Abundance from Exon Junction Microarray
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- Authors
- Pora Kim, S. June Oh, Sang Hyuk Lee
- Issue Date
- 2006-03
- Citation
- Genomics and Informatics, v.4, no.1, pp.33-39
- ISSN
- 1598-866X
- Publisher
- Korea genome organization
- Language
- English
- Type
- Journal Article
- Project Code
- 06MB1700, SW Component Development of Bio Data Mining & Integrated Management, Park Seon Hee
- Abstract
- Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microaray techniques There exist three types of microarrays interogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tisues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization infered from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NLS) fiting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.
- KSP Keywords
- Alternative splicing(AS), Array data, Cell line, Experimental Data, Expression data, Genome-wide survey, Least Squares(LS), Non-negative least squares, Nonnegative Matrix Factorization(NMF), Splice site, Tiling arrays