Functional And Pathway Analysis 2010
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The document discusses functional and pathway analysis in bioinformatics, particularly in relation to high-throughput genomics methods like microarrays and next-generation sequencing. It covers various enrichment analysis methods such as Singular Enrichment Analysis (SEA), Modular Enrichment Analysis (MEA), and Gene Set Enrichment Analysis (GSEA), detailing how these methods assess functional categories and pathways of genes. Additionally, it highlights different web-based tools and resources available for performing these analyses.
Functional And Pathway Analysis 2010
- 1. Functional and Pathway Analysis Stewart MacArthur Bioinformatics Core March 18th, 2010 Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 1 / 19
- 2. Introduction The Problem The Problem • High-throughput genomics methods: • microarrays • next generation sequencing • Generate large lists of “interesting” genes • How to we summarize? • What are the themes of the lists? Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 2 / 19
- 3. Introduction The Solution The Solution • Functional Analysis • Determine common functions • Find groups of functionally related genes • Pathways Analysis • Determine common pathways • Determine potential up/down stream regulators Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 3 / 19
- 4. Enrichment Analysis Methods The Methods Enrichment Analysis Are there more of the genes in my list in functional category X than we could expect by chance? • SEA - Singular Enrichment Analysis • MEA - Modular Enrichment Analysis • GSEA - Gene Set Enrichment Analysis Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 4 / 19
- 5. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 6. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 7. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 8. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 9. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 10. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 11. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 12. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 13. Enrichment Analysis Methods Hypergeometric Brief Aside: Hypergeometric Test The hypergeometric test calculates the probability that the number of genes in our gene list that are in functional category/pathway X occured by chance Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 5 / 19
- 14. Enrichment Analysis Methods SEA - Singular Enrichment Analysis SEA - Singular Enrichment Analysis Inputs: • List of “interesting” genes, e.g. DE genes • List of functional annotations e.g. GO annotations Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 6 / 19
- 15. Enrichment Analysis Methods SEA - Singular Enrichment Analysis SEA - Singular Enrichment Analysis Inputs: • List of “interesting” genes, e.g. DE genes • List of functional annotations e.g. GO annotations Method: For each annotation • Are more of the genes in our list present than would be expected by chance • Calculate p-value Next annotation • Correction for multiple testing Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 6 / 19
- 16. Enrichment Analysis Methods SEA - Singular Enrichment Analysis SEA - Singular Enrichment Analysis Inputs: • List of “interesting” genes, e.g. DE genes • List of functional annotations e.g. GO annotations Method: For each annotation • Are more of the genes in our list present than would be expected by chance • Calculate p-value Next annotation • Correction for multiple testing Output: • Ranked list of annotations Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 6 / 19
- 17. Enrichment Analysis Methods MEA - Modular Enrichment Analysis MEA - Modular Enrichment Analysis • Extension of SEA • Incorporates network discovery algorithms • Considers term-to-term relationships • Terms not treated as separate tests • Uses co-occurrences of terms • More closely related to biology • Based on assumption that related functional groups have similar member genes Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 7 / 19
- 18. Enrichment Analysis Methods GSEA -Gene Set Enrichment Analysis GSEA No cutoff, uses all genes ranked e.g. microarray experiment ranked by fold change or differential expression For each functional annotation • Are genes randomly distributed in ranked list? or • Are genes distributed towards the top/bottom of the list? • Calculate enrichment score (ES) • Calculate significance of ES Next annotation • Correct for multiple testing Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 8 / 19
- 19. Enrichment Analysis Methods GSEA -Gene Set Enrichment Analysis GSEA Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 9 / 19
- 20. Enrichment Analysis Methods GSEA -Gene Set Enrichment Analysis GSEA Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 9 / 19
- 21. Enrichment Analysis Methods GSEA -Gene Set Enrichment Analysis GSEA Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 9 / 19
- 22. Enrichment Analysis Methods GSEA -Gene Set Enrichment Analysis GSEA Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 9 / 19
- 23. Annotation Resources Annotation Resources Where do the gene sets come from? • GO - Gene Ontology • KEGG - Kyoto Encyclopedia of Genes and Genomes • MSigDB - Molecular Signatures Database • Pathway Commons • ... • ... Choice of annotation often dictated by choice of tool Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 10 / 19
- 24. Web based tools Tools • Approximately 68 enrichment tools Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 11 / 19
- 25. Web based tools Tools • Here they are: Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 11 / 19
- 26. Web based tools Tools • Mainly Web based Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 11 / 19
- 27. Web based tools Tools • Mainly Hypergeometric based Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 11 / 19
- 28. Web based tools Recommended Tools • SEA - ClueGO, GOStat, • MEA - DAVID, GOToolBox • GSEA - GeneTrail, FatiScan (Babelomics) See Bioinformatics Core Wiki Page for more tools http://criwiki.cancerresearchuk.org/ Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 12 / 19
- 29. Web based tools David DAVID http://david.abcc.ncifcrf.gov The Database for Annotation, Visualization and Integrated Discovery • Over 1,600 DAVID citations • 37 nature-branded citations to date • Daily Usage: 1200 gene lists/sublists • Daily Usage: 400 unique researchers. Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 13 / 19
- 30. Web based tools David DAVID http://david.abcc.ncifcrf.gov The Database for Annotation, Visualization and Integrated Discovery • Identify enriched biological themes • Discover enriched functional-related gene groups • Cluster redundant annotation terms • Visualize genes on BioCarta & KEGG pathway maps • Search for other functionally related genes not in the list • Convert gene identifiers from one type to another. • And more Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 14 / 19
- 31. Web based tools GeneTrail GeneTrail Annotations include • KEGG • TRANSPATH • TRANSFAC • GO Methods: • Over-Representation Analysis (ORA) • Gene Set Enrichment Analysis (GSEA) Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 15 / 19
- 32. Commercial Tools Ingenuity Pathways Analysis (IPA) Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 16 / 19
- 33. Commercial Tools GeneGo MetaCore Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 17 / 19
- 34. Commercial Tools Suraj - GeneGO Demo Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 18 / 19
- 35. Cytoscape Cytoscape Stewart MacArthur (Bioinformatics Core) Functional and Pathway Analysis March 18th, 2010 19 / 19