Difference between revisions of "Enrichment"
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:* Access the Web version of the article, it conveniently contains the required links. | :* Access the Web version of the article, it conveniently contains the required links. | ||
− | :* Use [http://david.abcc.ncifcrf.gov/helps/FAQs.html#demo '''Demo List 2], provided on the DAVID site for your analysis. Remember to read the description of the gene list. | + | :* Use [http://david.abcc.ncifcrf.gov/helps/FAQs.html#demo '''Demo List 2'''], provided on the DAVID site for your analysis. Remember to read the description of the gene list. |
:* Do not use any of the Java tools. <small>As of this writing Java applets in Web browsers are considered fundamentally insecure, they should be disabled in your browser.</small> | :* Do not use any of the Java tools. <small>As of this writing Java applets in Web browsers are considered fundamentally insecure, they should be disabled in your browser.</small> | ||
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==Further reading and resources== | ==Further reading and resources== | ||
{{#pmid: 21877285}} | {{#pmid: 21877285}} |
Revision as of 15:12, 27 January 2013
Enrichment Analysis
Enrichment analysis addresses the question: do genes in a set have a non-trivial property in common? The methodologies discussed here have applications in many fields of computational biology.
Contents
Introductory reading
Tilford & Siemers (2009) Gene set enrichment analysis. Methods Mol Biol 563:99-121. (pmid: 19597782) |
Relative Enrichment
Relative Enrichment is the ratio of (fraction of elements of interest in an observed set) and (fraction of elements of interest in a reference set).
Functional Annotation Analysis (FAA)
Functional Annotation Analysis (FAA) analyses the enrichment of properties in a set of genes. Such properties may include GO terms, EC codes, membership in pathways, coregulation etc. A good resource for FAA is the DAVID database and server.
Gene Set Enrichment Analysis (GSEA)
Gene Set Enrichment Analysis (GSEA) analyses the enrichment of members of a predefined gene set a set of experimentally observed genes. Such predefined gene sets may come from pathway components, interaction clusters, genes that have particular transcription factor binding sites in common etc. The default resource is the GSEA software, distributed via the Broad Institute GSEA homepage.
Exercises
Task:
- Work through the DAVID tutorial published in nature protocols:
Huang et al. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57. (pmid: 19131956) |
- Access the Web version of the article, it conveniently contains the required links.
- Use Demo List 2, provided on the DAVID site for your analysis. Remember to read the description of the gene list.
- Do not use any of the Java tools. As of this writing Java applets in Web browsers are considered fundamentally insecure, they should be disabled in your browser.
- For each of the analysis steps, think clearly about whether the results support od contradict your expectations about the data. Feel free to discuss your expectations and findings on the mailing list.
- If there are any problems with the assignment, contact me!
Further reading and resources
Merico et al. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781:257-77. (pmid: 21877285) |
Subramanian et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U.S.A 102:15545-50. (pmid: 16199517) |