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Object Groups & Enrichment Analysis
Suzanne Paley
Pathway Tools Workshop 2010
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What is an Object
G
roup?
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
G
roup?
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
G
roup?
Display it
Select which columns to include in table
Use as navigational aid
Export it
Table
S
equences (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
O
rganize groups into folders
Future work
Add object group capabilities to
BioCyc
website
Enable sharing of groups
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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