Splice Variant Search with Gene Expression Data
نویسندگان
چکیده
Alternative splicing is the phenomena that the pre-mRNA transcript from DNA is processed into different mRNAs by spliced different types of introns. The organism can acquire proteins as many times as genes. Therefore to find such splicing variants is risen in the post genome era. We investigate a new method to detect splicing variants with the gene expression data by the oligonucleotide array technology. Recently, the technology which measures concentrations of splice variant products respectively is proposed [2]. We focus on the alternative splicing observed among different tissues or different states. By comparing between tissues or states, we can find splicing variants. The oligonucleotide array, for example Affymetrix’s GeneChip, has dozens of probes for one gene. If you will find the exon skipping, at least one probe for one exon is needed. The ratio at this probe reflects the difference of the alternative product concentration between two conditions. Moreover, the more to prepare probes for a gene, the more to find detailed structure of splice variants. In general, the oligonucleotide array can store quite large number of probes on a chip. It is possible to find splice variants exhaustively. We will show in the following section that hot to detect the alternative splicing in the case of CD44 gene which has some types of action depend on the isoform [1].
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