A Practical Guide to Cancer Systems Biology

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  1. Proteomic Data Analysis 73


Interpret DAVID results (Fig. 10).

Figure 10. Interpret DAVID results. To perform EnrichmentMap of GSEA results, set
the parameters as follows: 1. Select “DAVID/BiNGO/Great” as analysis type; 2. Select
the expression TXT file; 3. Select DAVID result TXT file as the enrichments; 4. (Optional)
Adjust the parameters for cut-off significant enriched functions and function similarity; 5.
Click “Build” to perform EnrichmentMap.


Launch Cytoscape program, install EnrichmentMap App from App>
App Manager, and apply EnrichmentMap by click App>EnrichmentMap>
Create Enrichment Map.


References



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    proteomics: Ready for the big time.Nat. Methods7:681–685.

  2. Mann M and Kelleher NL. (2008) Precision proteomics: The case for high resolution
    and high mass accuracy.Proc. Natl. Acad. Sci. USA105:18132–18138.

  3. Cox J and Mann M. (2008) Maxquant enables high peptide identification rates,
    individualized ppb-range mass accuracies and proteome-wide protein quantification.
    Nat. Biotechnol.26:1367–1372.

  4. Keller A, Eng J, Zhang Net al.(2005) A uniform proteomics ms/ms analysis platform
    utilizing open xml file formats.Mol. Syst. Biol.1:2005.0017.

  5. Rauch A, Bellew M, Eng Jet al.(2006) Computational proteomics analysis system
    (cpas): An extensible, open-source analytic system for evaluating and publishing
    proteomic data and high throughput biological experiments.J. Proteome Res.5:
    112–121.

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