Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(Web Server issue):W300-W304; doi:10.1093/nar/gkp429
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W300-W304
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
GoGene: gene annotation in the fast lane
1Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany and 2Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287, USA
*To whom correspondence should be addressed. Tel: +49 351 463 400 60; Fax: +49 351 463 400 61; Email: conrad.plake{at}biotec.tu-dresden.de
Received January 30, 2009. Revised April 21, 2009. Accepted May 11, 2009.
High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4 000 000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18 000 000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins Nucleic Acids Res., November 12, 2009; (2009) gkp1042v1. [Abstract] [Full Text] [PDF]
|
|