PPT - Bioinformatics Research Group at SRI International

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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