PPT - Bioinformatics Research Group at SRI International

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Oct 2, 2013 (3 years and 8 months ago)

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SRI International Bioinformatics

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Object Groups & Enrichment Analysis

Suzanne Paley

Pathway Tools Workshop 2010

SRI International Bioinformatics

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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


SRI International Bioinformatics

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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


SRI International Bioinformatics

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SRI International Bioinformatics

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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


SRI International Bioinformatics

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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



SRI International Bioinformatics

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Transformation: Genes
-
> Pathways

SRI International Bioinformatics

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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.

SRI International Bioinformatics

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Enrichment Analysis


Groups
-
>
Transform
Group
-
>
Enrichment
Analysis

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Enrichment Results

SRI International Bioinformatics

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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