From Functional Genomics to Physiological Model: the Gene Ontology

1
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 Onto-Express Onto-Ex
press-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
2
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)