1. SRI International Bioinformatics 1 Object Groups & Enrichment Analysis Suzanne Paley Pathway Tools Workshop 2010

2. SRI International Bioinformatics 2 What is an Object Group? A set of objects that are interesting for any reason, e.g. l Set of genes upregulated in an expression experiment l Set of compounds in a pathway of interest or found in a particular cellular compartment l Set of pathways scheduled for further curation What can be in an object group? l Genes l Proteins/RNAs l Reactions l Pathways l Compounds l GO Terms

3. SRI International Bioinformatics 3 How to Create an Object Group? Groups -> Create New Group Type in list of objects l 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

4. SRI International Bioinformatics 4

5. 5 What can you do with an Object Group? Display it l Select which columns to include in table l Use as navigational aid Export it l Table l Sequences (for genes or proteins) l BioPAX (for pathways) l SBML (for reactions) Edit it l Manually add or delete objects l Filter by class l Give it a name and/or description Combine it with another group l Union, intersection, set difference Transform it

6. SRI International Bioinformatics 6 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

7. SRI International Bioinformatics 7 Transformation: Genes -> Pathways

8. SRI International Bioinformatics 8 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.

9. SRI International Bioinformatics 9 Enrichment Analysis Groups-> Transform Group -> Enrichment Analysis

10. SRI International Bioinformatics 10 Enrichment Results

11. SRI International Bioinformatics 11 Recent Enhancements & Future Work New in 14.5 l Organize groups into folders Future work l Add object group capabilities to BioCyc website l Enable sharing of groups u Groups could be marked public or private, or shared only with specified list of other users l Seamless access to groups whether via website or desktop software