1. 9/10/06 GO Users Meeting 2006 Seattle, Washington The AgBase GO Annotation Tools Susan Bridges 1,3, Fiona McCarthy 2,3, Nan Wang 1,3, G. Bryce Magee 1,3, Bindu Nanduri 2,3, Shane Burgess 2,3 1 Department of Computer Science & Engineering 2 College of Veterinary Medicine 3 Institute for Digital Biology

2. 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

3. AgBase.msstate.edu

6. 9/10/06 GO 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.

7. 9/10/06 GO Users Meeting 2006 Seattle, Washington The AgBase Tools

8. GOProfiler

9. 9/10/06 GO Users Meeting 2006 Seattle, Washington Unannotated Proteins

10. 9/10/06 GO Users Meeting 2006 Seattle, Washington Comparison of Levels of Annotation Rice Maize Tomato

11. 9/10/06 GO Users Meeting 2006 Seattle, Washington Protein Annotation Process Protein identifiers or Fasta format GORetriever Annotated Proteins GOanna Proteins with no annotations GOSlimViewer

13. 9/10/06 GO Users Meeting 2006 Seattle, Washington GOanna

14. 9/10/06 GO Users Meeting 2006 Seattle, Washington GOAnna Results

15. 9/10/06 GO Users Meeting 2006 Seattle, Washington GOSlimViewer GO ID list Selected GO Slim GOSlimViewer Text File Summary Plot Program

17. 9/10/06 GO Users Meeting 2006 Seattle, Washington Gene Expression Annotation Process Fasta sequence file Annotated Sequences + Alignments GOannaGOSlimViewer Manual Inspection of Alignments Selected Annotated Sequences Modeling of Results

18. 9/10/06 GO Users Meeting 2006 Seattle, Washington GOanna for EST sequences

19. 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

20. 9/10/06 GO 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%

21. 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

22. 9/10/06 GO 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