Skip Navigation



Bioinformatics Advance Access published online on August 20, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn440
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
24/20/2376    most recent
btn440v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Pu, S.
Right arrow Articles by Wodak, S. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pu, S.
Right arrow Articles by Wodak, S. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Local Coherence in Genetic Interaction Patterns Reveals Prevalent Functional Versatility

Shuye Pu 1,*, Karen Ronen 1, James Vlasblom 1, Jack Greenblatt 2,3 and Shoshana J. Wodak 1,3,4

1Molecular structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto ON, Canada M5G 1X8
2Terrence Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto ON, Canada, ON M5S 3E1
3Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8
4Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8

*To whom correspondence should be addressed. Dr. Shuye Pu, E-mail: shuyepu{at}sickkids.ca


  Abstract

Motivation: Epistatic or genetic interactions, representing the effects of mutating one gene on the phenotypes caused by mutations in one or more distinct genes, can be very helpful for uncovering functional relationships between genes. Recently, the Epistatic Miniarray Profiles (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. For E-MAP data analysis, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles, and the resulting descriptions assign each gene to only one group, thereby ignoring the multi-functional roles played by most genes.

Results: Here we present an original Local Coherence Detection (LCD) algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of gene function. The performance of our algorithm is illustrated by applying it to two E-MAP datasets and an E-MAP-like in silico dataset for the yeast S. cerevisiae. In addition to recapitulating the majority of the functional modules and many protein complexes reported previously, our algorithm uncovers many recently documented and novel multi-functional relationships between genes and gene groups. Our algorithm hence represents a valuable tool for uncovering new roles for genes with annotated functions and for mapping groups of genes and proteins into pathways.

Availability: A Java implementation of the LCD algorithm is available at URL http://genepro.ccb.sickkids.ca/biclustering.html.

Contact: shuyepu{at}sickkids.ca

Supplementary information: URL to be provided by the journal

Associate Editor: Dr. Trey Ideker

Received on May 13, 2008; revised on August 1, 2008; accepted on August 15, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.