Skip Navigation


Nucleic Acids Research Advance Access originally published online on May 8, 2009
Nucleic Acids Research 2009 37(Web Server issue):W350-W355; doi:10.1093/nar/gkp331
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3587K) Freely available
Right arrow Screen PDF (514K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/suppl_2/W350    most recent
gkp331v1
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 Sun, C.-H.
Right arrow Articles by Yi, G.-S.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sun, C.-H.
Right arrow Articles by Yi, G.-S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W350-W355
© 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

COFECO: composite function annotation enriched by protein complex data

Choong-Hyun Sun, Min-Sung Kim, Youngwoong Han and Gwan-Su Yi*

Department of Bio and Brain Engineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, South Korea

*To whom correspondence should be addressed. Tel: +82 42 866 6160; Fax: +82 42 866 6814; Email: gsyi{at}kaist.ac.kr

Received March 3, 2009. Revised April 13, 2009. Accepted April 20, 2009.

COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship of annotation terms can be more clearly delineated by integrating the information of physically interacting proteins with biological pathways and GO terms. COFECO has the following advanced characteristics: (i) The composite annotation sets of correlated functions and cellular processes for a given gene set can be identified in a more comprehensive and specified way by the employment of protein complex data together with GO and KEGG pathways as annotation resources. (ii) Orthology based integrative annotations among different species complement the defective annotations in an individual genome and provide the information of evolutionary conserved correlations. (iii) A term filtering feature enables users to collect the specified annotations enriched with selected function terms. (iv) A cross-comparison of annotation results between two different datasets is possible. In addition, COFECO provides a web-based GO hierarchical viewer and KEGG pathway viewer where the enrichment results can be summarized and further explored. COFECO is freely accessible at http://piech.kaist.ac.kr/cofeco.


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
A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, and H.-W. Mewes
CORUM: the comprehensive resource of mammalian protein complexes--2009
Nucleic Acids Res., November 1, 2009; (2009) gkp914v1.
[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.