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Activity Number: 578
Type: Invited
Date/Time: Thursday, August 7, 2014 : 8:30 AM to 10:20 AM
Sponsor: WNAR
Abstract #310799
Title: Clustering mRNA-Seq Samples for Alternative Splicing Detection
Author(s): Elizabeth Purdom*+ and Marla Johnson
Companies: University of California, Berkeley and University of California, Berkeley
Keywords: gene expression ; sequencing ; clustering ; multinomial clustering
Abstract:

The DNA encoded by a single gene can result in different distinct mRNA products or proteins called isoforms of the gene. Previous technologies for measuring mRNA could only measure the cumulative gene product across all cells, but current sequencing of mRNA can provide estimates of the levels of individual isoforms within the cell. It remains to adapt many standard statistical methods commonly used for analyzing gene expression levels for the context of isoforms. One novel question is whether we can find groupings or clusters of samples that are distinguished not by their gene expression but by their isoform usage. Such clusters in tumors, for example, could be the result of shared disruption to the splicing system that creates the different isoforms. We propose novel approaches to clustering mRNA-Seq data that identifies clusters of samples with common isoform usage. We show that our methods are more sensitive to finding clusters of similar alternative splicing patterns than standard clustering techniques applied directly to the estimates of isoform levels.


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