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Understanding Object Groups in Pathway Analysis: Tools & Techniques Workshop 2010

This workshop by Suzanne Paley focuses on Object Groups in biological analysis, emphasizing their creation, utility, and transformation. Object Groups can encompass genes, proteins, reactions, pathways, compounds, and GO terms, making them essential in research. Participants learn various methods to construct Object Groups, including extraction from datasets and manual methods. The session also keenly highlights enrichment analysis, showcasing how to assess significant pathways and GO terms related to selected groups. Recent enhancements and future developments are discussed, emphasizing collaborative features and integration with BioCyc.

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Understanding Object Groups in Pathway Analysis: Tools & Techniques Workshop 2010

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

  2. 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

  3. How to Create an Object Group? • 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

  4. 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

  5. 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

  6. Transformation: Genes -> Pathways

  7. 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.

  8. Enrichment Analysis • Groups-> Transform Group -> Enrichment Analysis

  9. Enrichment Results

  10. 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

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