Physical Address
IGBB
Portera HPC Building
2 Research Boulevard
Starkville, MS 39759
Mailing Address
IGBB
Portera HPC Building
Box 9627
Mississippi State, MS 39762
Phone/Fax
Phone: 662-325-8278
Fax: 662-325-7692
See Personnel for individual IGBB faculty and staff contact names/numbers/email addresses.
AgBase: a unified resource for functional analysis in agriculture
IGBB Authors:
Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, Bindu Nanduri, Mark L. Lawrence, Shane C. BurgessPUBLICATION YEAR:
2007IMPACT FACTOR:
7.444CITATION COUNT:
88McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC (2007) AgBase: a unified resource for functional analysis in agriculture.
Nucleic Acids Research 35(Database issue): D599-D603.
DOI:
10.1093/nar/gkl936EID:
2-s2.0-33846081387PMID: 17135208
DOWNLOAD PDFABSTRACTAnalysis 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 are available from the AgBase proteogenomics link. We contribute Gene Ontology (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 GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations.
Dr. Caleb LemleyAssociate Professor
Animal & Dairy SciencesIGBB Affiliate
email(662) 325-2934
Dr. Benjamin MagbanuaAssociate Professor
Civil & Environmental EngineeringIGBB Affiliate
email(662) 325-9777
website
The IGBB is supported, in part, by the following units:
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