9/10/06 go users meeting 2006 seattle, washington the agbase go annotation tools susan bridges 1,3,...
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9/10/06GO Users Meeting 2006
Seattle, Washington
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 & Engineering2College of Veterinary Medicine3Institute for Digital Biology
9/10/06GO 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
AgBase.msstate.edu
9/10/06GO Users Meeting 2006
Seattle, Washington
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.
9/10/06GO Users Meeting 2006
Seattle, Washington
The AgBase Tools
GOProfiler
9/10/06GO Users Meeting 2006
Seattle, Washington
Unannotated Proteins
9/10/06GO Users Meeting 2006
Seattle, Washington
Comparison of Levels of Annotation
Rice Maize
Tomato
9/10/06GO Users Meeting 2006
Seattle, Washington
Protein Annotation Process
Protein identifiers or Fasta format
GORetriever
Annotated Proteins
GOanna
Proteins with no annotations
GOSlimViewer
9/10/06GO Users Meeting 2006
Seattle, Washington
GOanna
9/10/06GO Users Meeting 2006
Seattle, Washington
GOAnna Results
9/10/06GO Users Meeting 2006
Seattle, Washington
GOSlimViewer
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Va35
Mp313E
GO ID list Selected GO Slim
GOSlimViewer
Text File Summary Plot Program
9/10/06GO Users Meeting 2006
Seattle, Washington
Gene Expression Annotation Process
Fasta sequence file
Annotated Sequences +Alignments
GOanna
GOSlimViewerManual Inspection of Alignments
Selected Annotated Sequences
Modeling of Results
9/10/06GO Users Meeting 2006
Seattle, Washington
GOanna for EST sequences
9/10/06GO 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
9/10/06GO Users Meeting 2006
Seattle, Washington
GO Annotation of Up-Regulated 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%
9/10/06GO 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
9/10/06GO Users Meeting 2006
Seattle, Washington
AgBase Team
Funding•Internal: MAFES, CVM, CSE, Office of Research•External: NIH, NSF, USDA
Bryce Magee Nan Wang Susan Bridges Shane Burgess Fiona McCarthy