1. Strategy for working on your own data sets.
Genomic Annotation and Functional Modeling Workshop
Maxwell H. Gluck Equine Research Center
15-16 November, 2011

4. Tutorial 1: Converting Accessions
Some resources for converting database accessions are described and to help you follow the tutorial, screenshots of these websites are provided in an accompanying Powerpoint presentation.

5. Tutorial 2: Retrieving GO
In this tutorial use the results of the ID mapping to retrieve GO annotation for our horse Entrez Gene data set.
Results are provided independently, if you wish to work on this tutorial independently.

6. Tutorial 3: GO Enrichment
GO enrichment analysis of previous data using DAVID.
GO enrichment analysis of bovine data using AgriGO.

7. Tutorial 4: Quantitative data
Use GOModeler to define the phenotype of specific populations of neoplastically-transformed cells.
Use AgriGO Parametric Analysis of Gene Set Enrichment (PAGE) to look at gene expression data.

8. Learning more about GO

9. Working on your own data:
ID mapping – what accessions do you have and what do you need to get GO for your data set (e.g., using GORetriever)?
Getting GO – use GORetriever
check how much of your data has GO
use GOSlimViewer to summarize?
GO Enrichment analysis
compare different tools using your data (e.g., DAVID, AgriGO, GOStat, etc)
What do these tools tell you about pathways, networks analysis, etc?

10. Important! AgBase provides continuing support after this workshop.
help/advice with strategies for modeling your data.
providing GO annotations for data sets upon request (esp. large data sets)
request access to tools under construction – looking to people to provide feedback
general assistance with biocomputing, e.g. specialized Blast searches, genome browsers, formatting.