Bioinformatics Advance Access published online on November 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl567
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
* To whom correspondence should be addressed.
Motivation: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing. Results: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical Hypergeometric test or a conditional Hypergeometric that uses the relationships among GO terms to decorrelate the results. Availability: GOstats is available as an R package from the Bioconductor project: http://bioconductor.org.
Received October 16, 2006
Accepted November 3, 2006
Applications note
Using GOstats to test gene lists for GO term association
S. Falcon 1 * and R. Gentleman 1
S. Falcon, E-mail: sfalcon{at}fhcrc.org
Abstract
Associate Editor: Trey Ideker
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H. Ramos, P. Shannon, and R. Aebersold The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data Bioinformatics, September 15, 2008; 24(18): 2110 - 2111. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. N. Holcomb, D. I. Grove, M. Kinnunen, C. L. Friedman, I. S. Gallaher, T. M. Morgan, C. L. Sather, J. J. Delrow, P. S. Nelson, P. H. Lange, et al. Genomic Alterations Indicate Tumor Origin and Varied Metastatic Potential of Disseminated Cells from Prostate Cancer Patients Cancer Res., July 15, 2008; 68(14): 5599 - 5608. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bauer, S. Grossmann, M. Vingron, and P. N. Robinson Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration Bioinformatics, July 15, 2008; 24(14): 1650 - 1651. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. D. Rand, C. E. Bland, and J. Bond Methylmercury Activates Enhancer-of-Split and Bearded Complex Genes Independent of the Notch Receptor Toxicol. Sci., July 1, 2008; 104(1): 163 - 176. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Horan, C. Jang, J. Bailey-Serres, R. Mittler, C. Shelton, J. F. Harper, J.-K. Zhu, J. C. Cushman, M. Gollery, and T. Girke Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis Plant Physiology, May 1, 2008; 147(1): 41 - 57. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Shriner, T. M. Baye, M. A. Padilla, S. Zhang, L. K. Vaughan, and A. E. Loraine Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies Nucleic Acids Res., March 27, 2008; 36(4): e26 - e26. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Cordero, M. Botta, and R. A. Calogero Microarray data analysis and mining approaches Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Sanges, F. Cordero, and R. A. Calogero oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language Bioinformatics, December 15, 2007; 23(24): 3406 - 3408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Grossmann, S. Bauer, P. N. Robinson, and M. Vingron Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis Bioinformatics, November 15, 2007; 23(22): 3024 - 3031. [Abstract] [Full Text] [PDF]
|
|