1. Strategies for functional modeling
TAMU GO Workshop
17 May 2010

2. Types of data sets and modeling
Commercial array data – more likely to have ID mapping to support functional modeling.
Custom/USDA array data – may need to do your own ID mapping: see examples on workshop page.
Proteomics data
RNA-Seq data sets – computational pipelines to assign GO (GOanna is limited; contact AgBase).
Real-time data or quantitative proteomics data – hypothesis testing.

4. Overview of Functional Modeling Strategy
Microarray Ids
Pathways and network analysis
Ingenuity Pathways Analysis (IPA)
Pathway Studio
Cytoscape
DAVID
ArrayIDer
Protein/Gene identifiers
GO Enrichment analysis
Ingenuity Pathways Analysis (IPA)
Pathway Studio
Cytoscape
DAVID
EasyGO/AgriGO
Onto-Express
Onto-Express-to-go (OE2GO)
GORetriever
GO annotations
Genes/Proteins with no GO annotations
GOSlimViewer
Yellow boxes represent AgBase tools
Green/Purple boxes are non-AgBase resources
GOanna

5. Functional Modeling Considerations
Should I add my own GO?
use GOSlimViewer to see how much GO is available for your species
use GORetriever to see how much GO is available for your dataset
Should I do GO analysis and pathway analysis and network analysis?
different functional modeling methods show different aspects about your data (complementary)
is this type of data available for your species (or a close ortholog)?
What tools should I use?
which tools have data for your species of interest?
what type of accessions are accepted?
availability (commercial and freely available)

6. Converting accessions
Depending on your data set & the tools you use, you are likely to need to convert between database accessions to do your functional modeling.
UniProt database – ID mapping tab
Ensembl BioMart
Online analysis tools:
DAVID
g:profiler
GORetriever
ArrayIDer – converts EST accessions

7. Converting accessions (cont’d)
Commercial arrays
Custom arrays
EST arrays
Proteomics
RNA-Seq data
Commercial ID mapping eg. NetAffy
Ensembl BioMart
Online tools (g:convert, DAVID)
ArrayIDer
UniProt ID Conversion

8. Working on your own data or examples:
Your own data set
retrieve existing GO (accession conversion?) & group using slim sets
try functional grouping (DAVID, AgriGO, etc)
New to GO
GO browser tutorials to familiarize yourself with GO
work on some example data sets
Example data sets

9. Your own data Start by retrieving existing GO (GORetriver)
may need to do accession conversion
GOanna – for sequence data sets
If you haven’t had results returned from GOanna, sample results are available in the example data sets
Try functional analysis using DAVID, AgriGO or etc
For help with hypothesis modeling etc, see me.

10. GO Browsers search for gene products search for GO terms
retrieve batch GO
some analysis tools (slim sets, enrichment analysis, etc)
QuickGO at EBI
AmiGO at GO Consortium
Does not include IEA annotations

12. Example Dataset 1 Chicken Affymetrix Array Converting Accessions
Retrieving GO annotations
Grouping using GOSlimViewer
GO term enrichment analysis using DAVID
GO term enrichment analysis using AgriGO

13. Example Dataset 2 EST Array and adding your own GO
Converting Accessions
Retrieving GO annotations
Adding GO annotations
GO enrichment analysis using additional GO annotations

14. What other information should we add to your workshop website??