From Functional Genomics to Physiological Model: the Gene Ontology - PowerPoint PPT Presentation

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From Functional Genomics to Physiological Model: the Gene Ontology

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Overview of Functional Modeling Strategy Microarray Ids Pathways and network analysis Ingenuity Pathways Analysis (IPA) Pathway Studio Cytoscape DAVID – PowerPoint PPT presentation

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Title: 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)
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