Transcript PPT - Bioinformatics Research Group at SRI International

Object Groups & Enrichment Analysis
Suzanne Paley
Pathway Tools Workshop 2010
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What is an Object Group?
A set of objects that are interesting for any reason,
e.g.
 Set of genes upregulated in an expression experiment
 Set of compounds in a pathway of interest or found in a particular
cellular compartment
 Set of pathways scheduled for further curation
 What can be in an object group?
 Genes
 Proteins/RNAs
 Reactions
 Pathways
 Compounds
 GO Terms
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How to Create an Object Group?
 Groups
-> Create New Group
 Type in list of objects
 Type in class name to include all instances of class
 Extract from Omics Dataset
 From file of gene names
 From Answer List
 By visiting object pages and adding them to
group from right-click menu
 By transforming or combining other groups
 Programmatically, using API
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What can you do with an Object
Group?
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Display it
 Select which columns to include in table
 Use as navigational aid
Export it
 Table
 Sequences (for genes or proteins)
 BioPAX (for pathways)
 SBML (for reactions)
Edit it
 Manually add or delete objects
 Filter by class
 Give it a name and/or description
Combine it with another group
 Union, intersection, set difference
Transform it
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Example Transformations
 All
genes in same transcription units
 Pathways, reactions of genes, compounds,
proteins
 Genes, compounds, proteins of pathways,
reactions
 GO terms of genes, genes annotated to GO terms
 Genes regulated by genes
 Enzymes activated/inhibited by compounds
 Enrichment analysis
 When
transforming, can either create new group
or modify existing group
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Transformation: Genes -> Pathways
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Enrichment Analysis
 Given
a group of genes, compute the set of GO
terms, pathways, and/or transcription factors that
are significantly enriched for that group relative to
the group of all genes in an organism.
 Given
a group of compounds compute the set of
pathways significantly enriched for that group
relative to the group of all compounds that
participate in pathways in an organism.
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Enrichment Analysis
 Groups->
Transform
Group ->
Enrichment
Analysis
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Enrichment Results
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Recent Enhancements & Future Work
 New
in 14.5
 Organize groups into folders
 Future
work
 Add object group capabilities to BioCyc website
 Enable sharing of groups
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Groups could be marked public or private, or shared only with
specified list of other users
Seamless access to groups whether via website or desktop
software
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