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The AgBase GO Annotation Tools Susan Bridges1,3, Fiona McCarthy2,3, Nan Wang1,3, G. Bryce Magee1,3, Bindu Nanduri2,3, Shane Burgess2,3 1Department of Computer Science & Engineering 2College of Veterinary Medicine 3Institute for Digital Biology 9/10/06 GO Users Meeting 2006 Seattle, Washington AgBase (www.agbase.msstate.edu) • Gene Ontology annotations of gene products from agricultural species • A suite of tools for functional analysis of proteomics and gene expression datasets 9/10/06 GO Users Meeting 2006 Seattle, Washington AgBase.msstate.edu AgBase Tools • Provides an integrated set of tools that enable scientists conducting research with agricultural species to analyze and model their data using GO • Tailored to the needs of users within the community. 9/10/06 GO Users Meeting 2006 Seattle, Washington The AgBase Tools 9/10/06 GO Users Meeting 2006 Seattle, Washington GOProfiler Unannotated Proteins 9/10/06 GO Users Meeting 2006 Seattle, Washington Comparison of Levels of Annotation Rice Maize Tomato 9/10/06 GO Users Meeting 2006 Seattle, Washington Protein Annotation Process Protein identifiers or Fasta format GORetriever Proteins with no annotations Annotated Proteins GOanna 9/10/06 GO Users Meeting 2006 Seattle, Washington GOSlimViewer GOanna 9/10/06 GO Users Meeting 2006 Seattle, Washington GOAnna Results 9/10/06 GO Users Meeting 2006 Seattle, Washington Text File Summary 9/10/06 Plot Program GO Users Meeting 2006 Seattle, Washington cell cycle protein modification carbohydrate metabolism lipid metabolism protein biosynthesis development response to endogenous nucleobase, nucleoside, signal transduction cell differentiation GOSlimViewer amino acid and derivative Selected GO Slim biosynthesis GO ID list response to abiotic cell organization GOSlimViewer 25 20 15 10 Va35 Mp313E 5 0 Gene Expression Annotation Process Fasta sequence file Selected Annotated Sequences Modeling of Results Manual Inspection of Alignments GOSlimViewer GOanna Annotated Sequences + Alignments 9/10/06 GO Users Meeting 2006 Seattle, Washington GOanna for EST sequences 9/10/06 GO Users Meeting 2006 Seattle, Washington Maize Case Study (Rowena Kelley MSU) • University of Arizona gene array • Comparison of gene expression of two inbred maize germlines – Aspergillus flavus resistant – Aspergillus flavus susceptible • Innoculated/uninnoculated ears 9/10/06 GO Users Meeting 2006 Seattle, Washington GO Annotation of UpRegulated Genes • Total of 256 up-regulated genes were used as input for GOanna • Parent sequences annotated – 51% of MP313E sequences annotated – 52% of VA35 sequences annotated • Source of annotation – – – – Maize 18% Rice 30% Arabidopsis 34% Other plants 18% 9/10/06 GO Users Meeting 2006 Seattle, Washington FUTURE DIRECTIONS • Improved integration of of tools • Add pairwise alignment of translated sequences • Easy construction of custom GOSlims • GOModeler tool for systems biology view of data 9/10/06 GO Users Meeting 2006 Seattle, Washington AgBase Team Bryce Magee Nan Wang Susan Bridges Shane Burgess Fiona McCarthy Funding •Internal: MAFES, CVM, CSE, Office of Research •External: NIH, NSF, USDA 9/10/06 GO Users Meeting 2006 Seattle, Washington