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Finding association rules of cis-regulatory elements involved in alternative splicing

Published: 23 March 2007 Publication History

Abstract

Alternative splicing (AS) is a major mechanism to generate protein diversity. A single gene might generate hundreds or even thousands of different proteins. Recently, powerful large-scale AS profiling microarrays have been developed, but computational methods which investigate the regulation of AS are still lagging behind. Researchers have focused on finding cis-regulatory motifs in pre-mRNA sequences. However, most studies are searching for single motifs, while many splicing events seem to be regulated by a combination of splicing factors.
In this paper, we use association rule mining to discover cis-regulatory motifs that are responsible for distinct alternative splicing patterns in 10 mouse tissues. The inferred association rules indicate that alternative splicing pattern in different tissues might be explained by different motif combinations. Many of our discovered cis-regulatory motif candidates coincide with known splicing factor binding sites.

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cover image ACM Conferences
ACMSE '07: Proceedings of the 45th annual ACM Southeast Conference
March 2007
574 pages
ISBN:9781595936295
DOI:10.1145/1233341
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Publication History

Published: 23 March 2007

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Author Tags

  1. alternative splicing
  2. association rule mining
  3. sequence motif
  4. splicing regulatory elements

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ACM SE07
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ACM SE07: ACM Southeast Regional Conference
March 23 - 24, 2007
North Carolina, Winston-Salem

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ACMSE '07 Paper Acceptance Rate 81 of 137 submissions, 59%;
Overall Acceptance Rate 502 of 1,023 submissions, 49%

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