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Object Groups & Enrichment Analysis

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

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Object Groups & Enrichment Analysis

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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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