Transcript Bridges - Gene Ontology Consortium

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