Skip Navigation



Bioinformatics Advance Access published online on November 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl567
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
23/2/257    most recent
btl567v1
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
Google Scholar
Right arrow Articles by Falcon, S.
Right arrow Articles by Gentleman, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Falcon, S.
Right arrow Articles by Gentleman, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
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

1 Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA

* To whom correspondence should be addressed.
S. Falcon, E-mail: sfalcon{at}fhcrc.org


  Abstract

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.

Associate Editor: Trey Ideker
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
 BioinformaticsHome page
Y. Choi and C. Kendziorski
Statistical methods for gene set co-expression analysis
Bioinformatics, November 1, 2009; 25(21): 2780 - 2786.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
K. R. Shockley, D. Witmer, S. L. Burgess-Herbert, B. Paigen, and G. A. Churchill
Effects of atherogenic diet on hepatic gene expression across mouse strains
Physiol Genomics, November 1, 2009; 39(3): 172 - 182.
[Abstract] [Full Text] [PDF]

Home page
 Biol. Reprod.Home page
N. Forde, F. Carter, T. Fair, M.A. Crowe, A.C.O. Evans, T.E. Spencer, F.W. Bazer, R. McBride, M.P. Boland, P. O'Gaora, et al.
Progesterone-Regulated Changes in Endometrial Gene Expression Contribute to Advanced Conceptus Development in Cattle
Biol Reprod, October 1, 2009; 81(4): 784 - 794.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. A. Verdugo, C. F. Deschepper, G. Munoz, D. Pomp, and G. A. Churchill
Importance of randomization in microarray experimental designs with Illumina platforms
Nucleic Acids Res., September 1, 2009; 37(17): 5610 - 5618.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
B. Kutlu, A. G. Kayali, S. Jung, G. Parnaud, D. Baxter, G. Glusman, N. Goodman, L. A. Behie, A. Hayek, and L. Hood
Meta-analysis of gene expression in human pancreatic islets after in vitro expansion
Physiol Genomics, September 1, 2009; 39(1): 72 - 81.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Schade, T. Rao, N. Dourdin, R. Lesurf, M. Hallett, R. D. Cardiff, and W. J. Muller
PTEN Deficiency in a Luminal ErbB-2 Mouse Model Results in Dramatic Acceleration of Mammary Tumorigenesis and Metastasis
J. Biol. Chem., July 10, 2009; 284(28): 19018 - 19026.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Du, G. Feng, J. Flatow, J. Song, M. Holko, W. A. Kibbe, and S. M. Lin
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
Bioinformatics, June 15, 2009; 25(12): i63 - i68.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
P. Novak, T. J. Jensen, J. C. Garbe, M. R. Stampfer, and B. W. Futscher
Stepwise DNA Methylation Changes Are Linked to Escape from Defined Proliferation Barriers and Mammary Epithelial Cell Immortalization
Cancer Res., June 15, 2009; 69(12): 5251 - 5258.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Wu and M Watson
CORNA: testing gene lists for regulation by microRNAs
Bioinformatics, March 15, 2009; 25(6): 832 - 833.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
J. I. Martin-Subero, M. Kreuz, M. Bibikova, S. Bentink, O. Ammerpohl, E. Wickham-Garcia, M. Rosolowski, J. Richter, L. Lopez-Serra, E. Ballestar, et al.
New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling
Blood, March 12, 2009; 113(11): 2488 - 2497.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
C. Pan, C. Kumar, S. Bohl, U. Klingmueller, and M. Mann
Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions
Mol. Cell. Proteomics, March 1, 2009; 8(3): 443 - 450.
[Abstract] [Full Text] [PDF]

Home page
 Circ Cardiovasc GenetHome page
D. R. Fermin, A. Barac, S. Lee, S. P. Polster, S. Hannenhalli, T. L. Bergemann, S. Grindle, D. B. Dyke, F. Pagani, L. W. Miller, et al.
Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure
Circ Cardiovasc Genet, December 1, 2008; 1(2): 117 - 125.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. G. Addinall, M. Downey, M. Yu, M. K. Zubko, J. Dewar, A. Leake, J. Hallinan, O. Shaw, K. James, D. J. Wilkinson, et al.
A Genomewide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae
Genetics, December 1, 2008; 180(4): 2251 - 2266.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
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]

Home page
 Cancer Res.Home page
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]

Home page
 BioinformaticsHome page
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]

Home page
 Toxicol SciHome page
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]

Home page
 Plant Physiol.Home page
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]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Brief Funct Genomic ProteomicHome page
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]

Home page
 BioinformaticsHome page
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]

Home page
 BioinformaticsHome page
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]


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.