Skip Navigation

Nucleic Acids Research 2005 33(10):3154-3164; doi:10.1093/nar/gki624
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1177K) Freely available
Right arrow Screen PDF (431K) Freely available
Right arrow Supplementary Material
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 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 Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ho Sui, S. J.
Right arrow Articles by Wasserman, W. W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ho Sui, S. J.
Right arrow Articles by Wasserman, W. W.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 2 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

Shannan J. Ho Sui1,2, James R. Mortimer3, David J. Arenillas1,4, Jochen Brumm1,5, Christopher J. Walsh1,2, Brian P. Kennedy4 and Wyeth W. Wasserman1,3,*

1Centre for Molecular Medicine and Therapeutics, University of British Columbia Vancouver, BC, Canada 2Genetics Graduate Program, University of British Columbia Vancouver, BC, Canada 3Merck Frosst Centre for Therapeutic Research Kirkland QC, Canada 4Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada 5Department of Statistics, University of British Columbia Vancouver, BC, Canada

*To whom correspondence should be addressed. Tel: +1 604 875 3812; Fax: +1 604 875 3819; Email: wyeth{at}cmmt.ubc.ca

Received April 5, 2005. Revised April 22, 2005. Accepted May 12, 2005.

Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes.


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
 Nucleic Acids ResHome page
H. G. Roider, B. Lenhard, A. Kanhere, S. A. Haas, and M. Vingron
CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses
Nucleic Acids Res., October 1, 2009; 37(19): 6305 - 6315.
[Abstract] [Full Text] [PDF]

Home page
 Circ Cardiovasc GenetHome page
J. Naukkarinen, E. Nilsson, H. A. Koistinen, S. Soderlund, V. Lyssenko, A. Vaag, P. Poulsen, L. Groop, M.-R. Taskinen, and L. Peltonen
Functional Variant Disrupts Insulin Induction of USF1: Mechanism for USF1-Associated Dyslipidemias
Circ Cardiovasc Genet, October 1, 2009; 2(5): 522 - 529.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
W.-P. Lee and W.-S. Tzou
Computational methods for discovering gene networks from expression data
Brief Bioinform, July 1, 2009; 10(4): 408 - 423.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Zambelli, G. Pesole, and G. Pavesi
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W247 - W252.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J. B. Boonyaratanakornkit, E. J. Bartlett, E. Amaro-Carambot, P. L. Collins, B. R. Murphy, and A. C. Schmidt
The C Proteins of Human Parainfluenza Virus Type 1 (HPIV1) Control the Transcription of a Broad Array of Cellular Genes That Would Otherwise Respond to HPIV1 Infection
J. Virol., February 15, 2009; 83(4): 1892 - 1910.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
C. T. Fulp, G. Cho, E. D. Marsh, I. M. Nasrallah, P. A. Labosky, and J. A. Golden
Identification of Arx transcriptional targets in the developing basal forebrain
Hum. Mol. Genet., December 1, 2008; 17(23): 3740 - 3760.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Respir. Crit. Care Med.Home page
M. O. Leonard, K. Howell, S. F. Madden, C. M. Costello, D. G. Higgins, C. T. Taylor, and P. McLoughlin
Hypoxia Selectively Activates the CREB Family of Transcription Factors in the In Vivo Lung
Am. J. Respir. Crit. Care Med., November 1, 2008; 178(9): 977 - 983.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
Y. S. Lee, K. E. Latham, and C. A. VandeVoort
Effects of in vitro maturation on gene expression in rhesus monkey oocytes
Physiol Genomics, October 8, 2008; 35(2): 145 - 158.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Gotea and I. Ovcharenko
DiRE: identifying distant regulatory elements of co-expressed genes
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W133 - W139.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Thomas-Chollier, O. Sand, J.-V. Turatsinze, R. Janky, M. Defrance, E. Vervisch, S. Brohee, and J. van Helden
RSAT: regulatory sequence analysis tools
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W119 - W127.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Bourdeau, J. Deschenes, D. Laperriere, M. Aid, J. H. White, and S. Mader
Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells
Nucleic Acids Res., January 17, 2008; 36(1): 76 - 93.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. C. Bryne, E. Valen, M.-H. E. Tang, T. Marstrand, O. Winther, I. da Piedade, A. Krogh, B. Lenhard, and A. Sandelin
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D102 - D106.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, et al.
ORegAnno: an open-access community-driven resource for regulatory annotation
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D107 - D113.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. N. Singh, L.-S. Wang, and S. Hannenhalli
TREMOR a tool for retrieving transcriptional modules by incorporating motif covariance
Nucleic Acids Res., December 18, 2007; 35(21): 7360 - 7371.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. J. Ho Sui, D. L. Fulton, D. J. Arenillas, A. T. Kwon, and W. W. Wasserman
oPOSSUM: integrated tools for analysis of regulatory motif over-representation
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W245 - W252.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
N. A. Kolchanov, T. I. Merkulova, E. V. Ignatieva, E. A. Ananko, D. Yu. Oshchepkov, V. G. Levitsky, G. V. Vasiliev, N. V. Klimova, V. M. Merkulov, and T. C. Hodgman
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes
Brief Bioinform, July 12, 2007; (2007) bbm027v1.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. X. Jin, H. O'Geen, S. Iyengar, R. Green, and P. J. Farnham
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
Genome Res., June 1, 2007; 17(6): 807 - 817.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
S. P. Tabruyn, C. Sabatel, N.-Q.-N. Nguyen, C. Verhaeghe, K. Castermans, L. Malvaux, A. W. Griffioen, J. A. Martial, and I. Struman
The Angiostatic 16K Human Prolactin Overcomes Endothelial Cell Anergy and Promotes Leukocyte Infiltration via Nuclear Factor-{kappa}B Activation
Mol. Endocrinol., June 1, 2007; 21(6): 1422 - 1429.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. B. Jeffery, S. F. Madden, P. A. McGettigan, G. Perriere, A. C. Culhane, and D. G. Higgins
Integrating transcription factor binding site information with gene expression datasets
Bioinformatics, February 1, 2007; 23(3): 298 - 305.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. S. Bais, S. Grossmann, and M. Vingron
Simultaneous alignment and annotation of cis-regulatory regions
Bioinformatics, January 15, 2007; 23(2): e44 - e49.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
N. Radoja, A. Gazel, T. Banno, S. Yano, and M. Blumenberg
Transcriptional profiling of epidermal differentiation
Physiol Genomics, January 12, 2007; 27(1): 65 - 78.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-H. Peng, J.-T. Hsu, Y.-S. Chung, Y.-J. Lin, W.-Y. Chow, D. F. Hsu, and C. Y. Tang
Identification of degenerate motifs using position restricted selection and hybrid ranking combination
Nucleic Acids Res., December 2, 2006; 34(22): 6379 - 6391.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. X. Jin, A. Rabinovich, S. L. Squazzo, R. Green, and P. J. Farnham
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1
Genome Res., December 1, 2006; 16(12): 1585 - 1595.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
X. Yang, E. E. Schadt, S. Wang, H. Wang, A. P. Arnold, L. Ingram-Drake, T. A. Drake, and A. J. Lusis
Tissue-specific expression and regulation of sexually dimorphic genes in mice
Genome Res., August 1, 2006; 16(8): 995 - 1004.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Gazel, T. Banno, R. Walsh, and M. Blumenberg
Inhibition of JNK Promotes Differentiation of Epidermal Keratinocytes
J. Biol. Chem., July 21, 2006; 281(29): 20530 - 20541.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Kankainen, P. Pehkonen, P. Rosenstom, P. Toronen, G. Wong, and L. Holm
POXO: a web-enabled tool series to discover transcription factor binding sites.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W534 - W540.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. C. Newman, A. D. Bailey, and A. M. Weiner
Cockayne syndrome group B protein (CSB) plays a general role in chromatin maintenance and remodeling
PNAS, June 20, 2006; 103(25): 9613 - 9618.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. K. Mulligan, I. Ponomarev, R. J. Hitzemann, J. K. Belknap, B. Tabakoff, R. A. Harris, J. C. Crabbe, Y. A. Blednov, N. J. Grahame, T. J. Phillips, et al.
Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis
PNAS, April 18, 2006; 103(16): 6368 - 6373.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L.-W. Chang, R. Nagarajan, J. A. Magee, J. Milbrandt, and G. D. Stormo
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
Genome Res., March 1, 2006; 16(3): 405 - 413.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. B. Montgomery, O. L. Griffith, M. C. Sleumer, C. M. Bergman, M. Bilenky, E. D. Pleasance, Y. Prychyna, X. Zhang, and S. J. M. Jones
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
Bioinformatics, March 1, 2006; 22(5): 637 - 640.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Vlieghe, A. Sandelin, P. J. De Bleser, K. Vleminckx, W. W. Wasserman, F. van Roy, and B. Lenhard
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D95 - D97.
[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.