Protocol | Published:

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Nature Protocols 4, 44–57 (2009) | Download Citation

Subjects

Abstract

DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

Rent or Buy

All prices are NET prices.

References

  1. 1.

    et al. DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35, W169–W175 (2007).

  2. 2.

    et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 4, P3 (2003).

  3. 3.

    , , , & Identifying biological themes within lists of genes with EASE. Genome Biol. 4, R70 (2003).

  4. 4.

    et al. High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of common variable immune deficiency (CVID). BMC Bioinformatics 6, 168 (2005).

  5. 5.

    & GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20, 1464–1465 (2004).

  6. 6.

    , , & Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res. 32, W449–W456 (2004).

  7. 7.

    et al. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol. 5, R101 (2004).

  8. 8.

    , & FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578–580 (2004).

  9. 9.

    , & GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res. 33, W717–W723 (2005).

  10. 10.

    , & GObar: a gene ontology based analysis and visualization tool for gene sets. BMC Bioinformatics 6, 189 (2005).

  11. 11.

    et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).

  12. 12.

    & Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21, 3587–3595 (2005).

  13. 13.

    et al. DAVID knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 8, 426 (2007).

  14. 14.

    et al. The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8, R183 (2007).

  15. 15.

    , & DAVID gene ID conversion tool. Bioinformation 2, 428–430 (2008).

  16. 16.

    et al. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc. Natl. Acad. Sci. USA 99, 9380–9385 (2002).

Download references

Acknowledgements

We are grateful to the referees for their constructive comments and thank Robert Stephens, David Bryant and David Liu in the ABCC group for Web server support. Thanks also go to Xin Zheng and Jun Yang in the Laboratory of Immunopathogenesis and Bioinformatics (LIB) group for discussion. We also thank Bill Wilton and Mike Tartakovsky for information technology and network support. The project has been funded with federal funds from the National Institute of Allergy and Infectious Diseases (NIAID) and National Institutes of Health (NIH), under Contract no. NO1-CO-56000. The annotation of this tool and publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the United States Government.

Author information

    • Da Wei Huang
    •  & Brad T Sherman

    These authors contributed equally to this work.

Affiliations

  1. Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.

    • Da Wei Huang
    • , Brad T Sherman
    •  & Richard A Lempicki

Authors

  1. Search for Da Wei Huang in:

  2. Search for Brad T Sherman in:

  3. Search for Richard A Lempicki in:

Corresponding authors

Correspondence to Da Wei Huang or Richard A Lempicki.

Supplementary information

Excel files

  1. 1.

    Supplementary Data 1. Collection of ∼68 similar enrichment analysis tools. The tools are roughly categorized into three classes according to their backend algorithms. Reference links are provided for more information about each tool.

  2. 2.

    Supplementary Data 2. ∼400 Affymetrix IDs16 used in this paper

  3. 3.

    Supplementary Data 4. Summaries of gene identifier types and annotation categories supported in the DAVID system.

PDF files

  1. 1.

    Supplementary Data 3. Comparisons of the enrichment p-values between gene lists derived from microarray study vs. same size gene lists generated randomly. A 'good' gene lists should consistently contain more enriched biology than that of random list of the same sizes.

  2. 2.

    Supplementary Data 5. Screen shots of each major analysis step according to the description in the manuscript.

  3. 3.

    Supplementary Data 6. Examples for the input formats of a gene list.

To obtain permission to re-use content from this article visit RightsLink.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nprot.2008.211

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.