SRI International Bioinformatics 1 Object Groups & Enrichment Analysis Suzanne Paley Pathway Tools...

SRI International Bioinformatics1

Object Groups & Enrichment Analysis

Suzanne Paley

Pathway Tools Workshop 2010


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


How to Create an Object Group?

Groups -> Create New GroupType in list of objects

Type in class name to include all instances of classExtract from Omics DatasetFrom file of gene namesFrom Answer ListBy visiting object pages and adding them to

group from right-click menuBy transforming or combining other groupsProgrammatically, using API


What can you do with an Object Group?

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


Example Transformations

All genes in same transcription unitsPathways, reactions of genes, compounds,

proteinsGenes, compounds, proteins of pathways,

reactionsGO terms of genes, genes annotated to GO termsGenes regulated by genesEnzymes activated/inhibited by compoundsEnrichment analysis

When transforming, can either create new group or modify existing group


Transformation: Genes -> Pathways


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.


Enrichment Analysis

Groups-> Transform Group -> Enrichment Analysis


Enrichment Results


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

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

SRI International Bioinformatics 1 Object Groups & Enrichment Analysis Suzanne Paley Pathway Tools...

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