AgBase: supporting functional modeling in agricultural organisms

AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

[1]  Juan Miguel García-Gómez,et al.  Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research , 2005, Bioinform..

[2]  T. Buza,et al.  Gene Ontology annotation quality analysis in model eukaryotes , 2008, Nucleic acids research.

[3]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[4]  Jacob D. Jaffe,et al.  Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.

[5]  Carl J. Schmidt,et al.  eGIFT: Mining Gene Information from the Literature , 2010, BMC Bioinformatics.

[6]  Michael Y. Galperin,et al.  The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources , 2009, Nucleic Acids Res..

[7]  L. Stein,et al.  Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages , 2005, Comparative and functional genomics.

[8]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[9]  Shane C. Burgess,et al.  Structural and functional-annotation of an equine whole genome oligoarray , 2009 .

[10]  Nan Wang,et al.  Gene Model Detection Using Mass Spectrometry , 2010, Proteome Bioinformatics.

[11]  Purvesh Khatri,et al.  Onto-Tools: new additions and improvements in 2006 , 2007, Nucleic Acids Res..

[12]  Purvesh Khatri,et al.  Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments , 2004, Nucleic Acids Res..

[13]  Shane C. Burgess,et al.  Facilitating functional annotation of chicken microarray data , 2009, BMC Bioinformatics.

[14]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[15]  Bindu Nanduri,et al.  HPIDB - a unified resource for host-pathogen interactions , 2010, BMC Bioinformatics.

[16]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[17]  Winston A Hide,et al.  Big data: The future of biocuration , 2008, Nature.

[18]  Hedi Peterson,et al.  g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments , 2007, Nucleic Acids Res..

[19]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[20]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[21]  D. Maglott,et al.  The chicken gene nomenclature committee report , 2009, BMC Genomics.

[22]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[23]  F. McCarthy,et al.  Modeling a whole organ using proteomics: The avian bursa of Fabricius , 2006, Proteomics.

[24]  Susan M. Bridges,et al.  Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize , 2010, BMC Bioinformatics.

[25]  Rachael P. Huntley,et al.  The GOA database in 2009—an integrated Gene Ontology Annotation resource , 2008, Nucleic Acids Res..

[26]  Giorgio Valle,et al.  The Gene Ontology in 2010: extensions and refinements , 2009, Nucleic Acids Res..

[27]  Ron Edgar,et al.  Gene Expression Omnibus ( GEO ) : Microarray data storage , submission , retrieval , and analysis , 2008 .

[28]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[29]  Jacob D. Jaffe,et al.  The complete genome and proteome of Mycoplasma mobile. , 2004, Genome research.

[30]  Nan Wang,et al.  AgBase: a unified resource for functional analysis in agriculture , 2006, Nucleic Acids Res..

[31]  Bindu Nanduri,et al.  Prediction of peptides observable by mass spectrometry applied at the experimental set level , 2007, BMC Bioinformatics.

[32]  Nan Wang,et al.  AgBase: a functional genomics resource for agriculture , 2006, BMC Genomics.

[33]  T. J. Jankun-Kelly,et al.  GOModeler- A tool for hypothesis-testing of functional genomics datasets , 2010, BMC Bioinformatics.

[34]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[35]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[36]  Shane C. Burgess,et al.  ArrayIDer: automated structural re-annotation pipeline for DNA microarrays , 2009, BMC Bioinformatics.

[37]  Shane C. Burgess,et al.  Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data , 2010, PloS one.

[38]  T. Speed,et al.  GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.

[39]  Li Ni,et al.  The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species , 2009, PLoS Comput. Biol..

[40]  T. J. Jankun-Kelly,et al.  Exploratory visual analysis of conserved domains on multiple sequence alignments , 2009, BMC Bioinformatics.

[41]  Nan Wang,et al.  ProtQuant: a tool for the label-free quantification of MudPIT proteomics data , 2007, BMC Bioinformatics.