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United States Department of Agriculture

Agricultural Research Service

Title: AgBase: a unified resource for functional analysis in agriculture

Authors
item Mccarthy, F - MISSISSIPPI STATE UNIV
item Bridges, S - MISSISSIPPI STATE UNIV
item Wang, N - MISSISSIPPI STATE UNIV
item Magee, G - MISSISSIPPI STATE UNIV
item Williams, William
item Luthe, D - PENN STATE UNIVERSITY
item Burgess, S - MISSISSIPPI STATE UNIV

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 10, 2006
Publication Date: January 1, 2007
Citation: McCarthy, F.M., Bridges, S.M., Wang, N., Magee, G.B., Williams, W.P., Luthe, D.S., Burgess, S.C. 2007. AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Research. 35:D599-D603.

Interpretive Summary: Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource “AgBase” (www.agbase.msstate.edu). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data is available from the AgBase proteogenomics link. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the Gene Ontology (GO) is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an on-line mechanism for agricultural researchers to submit requests for GO annotations. AgBase is directly relevant for researchers in fields as diverse as agricultural production, cancer biology, human health, and evolutionary biology.

Technical Abstract: Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource “AgBase” (www.agbase.msstate.edu). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data is available from the AgBase proteogenomics link. We contribute GO annotations and we provide a two tier system of GO annotations for users. The “GO Consortium” gene association file contains the most rigorous GO annotations based solely on experimental data. The “Community” gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the Gene Ontology (GO) is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an on-line mechanism for agricultural researchers to submit requests for GO annotations.

Last Modified: 4/15/2014
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