Strategies for functional modeling

TAMU GO Workshop17 May 2010

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.

Protein/Gene identifiers

GORetriever

GO annotations

Genes/Proteins with no GO annotations

GOanna

Pathways and network analysis

GO Enrichment analysis

ArrayIDer

Microarray Ids

GOSlimViewer

Yellow boxes represent AgBase toolsGreen/Purple boxes are non-AgBase resources

Ingenuity Pathways Analysis (IPA)Pathway StudioCytoscapeDAVID

Ingenuity Pathways Analysis (IPA)Pathway StudioCytoscapeDAVIDEasyGO/AgriGOOnto-ExpressOnto-Express-to-go (OE2GO)

Overview of Functional Modeling Strategy

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)

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

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

Working on your own data or examples:

1. Your own data set retrieve existing GO (accession conversion?) &

group using slim sets try functional grouping (DAVID, AgriGO, etc)

2. New to GO GO browser tutorials to familiarize yourself with

GO work on some example data sets

3. Example data sets

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.

GO Browsers search for gene products search for GO terms retrieve batch GO some analysis tools (slim sets, enrichment

analysis, etc) QuickGO at EBI

http://www.ebi.ac.uk/QuickGO/ AmiGO at GO Consortium

http://amigo.geneontology.org Does not include IEA annotations

Example Dataset 1Chicken Affymetrix Array

1. Converting Accessions2. Retrieving GO annotations3. Grouping using GOSlimViewer4. GO term enrichment analysis using DAVID5. GO term enrichment analysis using AgriGO

Example Dataset 2EST Array and adding your own GO

1. Converting Accessions2. Retrieving GO annotations3. Adding GO annotations4. GO enrichment analysis using additional GO

annotations

What other information

should we add to your

workshop website??