OntologyTraverser: an R package for GO analysis
- PMID: 15333457
- DOI: 10.1093/bioinformatics/bth495
OntologyTraverser: an R package for GO analysis
Abstract
Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser--an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool.
Availability: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible.
Contact: cashaw@bcm.tmc.edu
Similar articles
-
Using GOstats to test gene lists for GO term association.Bioinformatics. 2007 Jan 15;23(2):257-8. doi: 10.1093/bioinformatics/btl567. Epub 2006 Nov 10. Bioinformatics. 2007. PMID: 17098774
-
AliasServer: a web server to handle multiple aliases used to refer to proteins.Bioinformatics. 2004 Sep 22;20(14):2331-2. doi: 10.1093/bioinformatics/bth241. Epub 2004 Apr 1. Bioinformatics. 2004. PMID: 15059813
-
GOChase: correcting errors from Gene Ontology-based annotations for gene products.Bioinformatics. 2005 Mar;21(6):829-31. doi: 10.1093/bioinformatics/bti106. Epub 2004 Oct 28. Bioinformatics. 2005. PMID: 15513987
-
Get ready to GO! A biologist's guide to the Gene Ontology.Brief Bioinform. 2005 Sep;6(3):298-304. doi: 10.1093/bib/6.3.298. Brief Bioinform. 2005. PMID: 16212777 Review.
-
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.BMC Bioinformatics. 2007 May 9;8 Suppl 3(Suppl 3):S5. doi: 10.1186/1471-2105-8-S3-S5. BMC Bioinformatics. 2007. PMID: 17493288 Free PMC article. Review.
Cited by
-
BayGO: Bayesian analysis of ontology term enrichment in microarray data.BMC Bioinformatics. 2006 Feb 23;7:86. doi: 10.1186/1471-2105-7-86. BMC Bioinformatics. 2006. PMID: 16504085 Free PMC article.
-
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25. Nucleic Acids Res. 2009. PMID: 19033363 Free PMC article.
-
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.Sci Rep. 2020 Oct 7;10(1):16672. doi: 10.1038/s41598-020-73326-3. Sci Rep. 2020. PMID: 33028846 Free PMC article.
-
WEGO: a web tool for plotting GO annotations.Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7. doi: 10.1093/nar/gkl031. Nucleic Acids Res. 2006. PMID: 16845012 Free PMC article.
-
FUNC: a package for detecting significant associations between gene sets and ontological annotations.BMC Bioinformatics. 2007 Feb 6;8:41. doi: 10.1186/1471-2105-8-41. BMC Bioinformatics. 2007. PMID: 17284313 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
