Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

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

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: An example layout of DAVID gene name batch viewer.
Figure 2: An example layout of DAVID gene functional classification.
Figure 3: An example layout of DAVID annotation chart.
Figure 4: An example layout of DAVID functional annotation clustering.
Figure 5: An example layout of DAVID Annotation Table.
Figure 6: Analytic tools/modules in DAVID.
Figure 7: Submit a gene list to DAVID and access various analytic tools/modules.
Figure 8: Pathway map viewer.

Similar content being viewed by others

References

  1. Huang da, W. 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).

    Article  Google Scholar 

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

    Article  Google Scholar 

  3. Hosack, D.A., Dennis, G. Jr., Sherman, B.T., Lane, H.C. & Lempicki, R.A. Identifying biological themes within lists of genes with EASE. Genome Biol. 4, R70 (2003).

    Article  Google Scholar 

  4. Zeeberg, B.R. 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).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  6. Khatri, P., Bhavsar, P., Bawa, G. & Draghici, S. 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).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  8. Al-Shahrour, F., Diaz-Uriarte, R. & Dopazo, J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578–580 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Lee, J.S., Katari, G. & Sachidanandam, R. GObar: a gene ontology based analysis and visualization tool for gene sets. BMC Bioinformatics 6, 189 (2005).

    Article  Google Scholar 

  11. Subramanian, A. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. Sherman, B.T. 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).

    Article  Google Scholar 

  14. Huang da, W. 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).

    Article  Google Scholar 

  15. Huang, D.W., Sherman, B.T. & Lempicki, R.A. DAVID gene ID conversion tool. Bioinformation 2, 428–430 (2008).

    Article  Google Scholar 

  16. Cicala, C. 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).

    Article  CAS  Google Scholar 

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

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Da Wei Huang or Richard A Lempicki.

Supplementary information

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. (XLS 101 kb)

Supplementary Data 2.

400 Affymetrix IDs16 used in this paper (XLS 71 kb)

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. (PDF 338 kb)

Supplementary Data 4.

Summaries of gene identifier types and annotation categories supported in the DAVID system. (XLS 38 kb)

Supplementary Data 5.

Screen shots of each major analysis step according to the description in the manuscript. (PDF 1600 kb)

Supplementary Data 6.

Examples for the input formats of a gene list. (PDF 69 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huang, D., Sherman, B. & Lempicki, R. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44–57 (2009). https://doi.org/10.1038/nprot.2008.211

Download citation

  • Published:

  • Issue Date:

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

This article is cited by

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.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing