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Bioinformatics

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Splicing arrays is a collaborative project between my lab and Prof. Xiang-Dong Fu's lab at UCSD

mRNA isoforms that arise as a result of alternative splicing provide a more complete picture of the transcriptome as they are capable of being translated into unique functional protein products. Alternative splicing is a very common phenomenon in the human genome, and many genes display differential expression of their spliced forms in cancerous and normal tissues. The expression of an isoform reflects to a greater degree the sum total of the processing a Pre-mRNA undergoes and can thus be used as a better indicator in distinguishing a normal tissue from a cancerous tissue. In a recent study we had used mRNA isoforms expression to identify biomarkers for prostate cancer (Li et.al., Cancer Res 66(8): 4079-88, 2006).The isoform exression data were obtained from splicing arrays. Currently we are using rigorously statistical methods to analyze the isoform expression data to understand the variability and heterogeneity associated with the expression levels in i. prostate cancer cell lines and non-prostate cancer cell lines and ii. normal and prostate cancer tissue. Our recent results show that there were several isoforms that showed significant differences in expression even in a within class comparison. We were also able to successfully identify isoforms with similar changes in expression levels, that when used as features for classification was able to provide robust class separation.

MAASE server is available at http://splice.bioinformatics.iusb.edu