Skip Navigation


Bioinformatics Advance Access originally published online on May 26, 2005
Bioinformatics 2005 21(15):3286-3293; doi:10.1093/bioinformatics/bti515
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/15/3286    most recent
bti515v1
Right arrow Alert me when this article is cited
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (5)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Flaherty, P.
Right arrow Articles by Arkin, A. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Flaherty, P.
Right arrow Articles by Arkin, A. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A latent variable model for chemogenomic profiling

Patrick Flaherty 1,*, Guri Giaever 3, Jochen Kumm 3, Michael I. Jordan 2 and Adam P. Arkin 4

1Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA
2Division of Computer Science, Department of Statistics, University of California Berkeley, CA 94720, USA
3Stanford Genome Technology Center, Stanford University School of Medicine Palo Alto, CA 94304, USA
4Department of Bioengineering, University of California and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute Berkeley, CA 94720, USA

*To whom correspondence should be addressed.

Motivation: In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure.

Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that requires genes to belong to a single cluster. Drugs such as miconazole and fenpropimorph that have different targets but similar off-target genes are clustered more accurately by the model-based framework. We show that this model is useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles.

Availability: Supplementary information and computer code at http://genomics.lbl.gov/llda

Contact: flaherty{at}berkeley.edu

Received on July 28, 2004; revised on May 11, 2005; accepted on May 23, 2005

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


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
K. Thevissen, K. R. Ayscough, A. M. Aerts, W. Du, K. De Brucker, E. M. K. Meert, J. Ausma, M. Borgers, B. P. A. Cammue, and I. E. J. A. Francois
Miconazole Induces Changes in Actin Cytoskeleton prior to Reactive Oxygen Species Induction in Yeast
J. Biol. Chem., July 27, 2007; 282(30): 21592 - 21597.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J.-G. Joung, D. Shin, R. H. Seong, and B.-T. Zhang
Identification of regulatory modules by co-clustering latent variable models: stem cell differentiation
Bioinformatics, August 15, 2006; 22(16): 2005 - 2011.
[Abstract] [Full Text] [PDF]


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.