Extracting Biological Meaning from Large Gene Lists with DAVID

Da Wei Huang1, Brad T. Sherman1, Xin Zheng1, Jun Yang1, Tomozumi Imamichi1, Robert Stephens1, Richard A. Lempicki1

1 National Cancer Institute at Frederick, Frederick, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.11
DOI:  10.1002/0471250953.bi1311s27
Online Posting Date:  September, 2009
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Abstract

High‐throughput genomics screening studies, such as microarray, proteomics, etc., often result in large, “interesting” gene lists, ranging in size from hundreds to thousands of genes. Given the challenges of functionally interpreting such large gene lists, it is necessary to incorporate bioinformatics tools in the analysis. DAVID is a Web‐based application that provides a high‐throughput and integrative gene functional annotation environment to systematically extract biological themes behind large gene lists. High‐throughput gene functional analysis with DAVID will provide important insights that allow investigators to understand the biological themes within their given genomic study. This unit will describe step‐by‐step procedures to use DAVID tools, as well as a brief rationale and key parameters in the DAVID analysis. Curr. Protoc. Bioinform. 27:13.11.1‐13.11.13. © 2009 by John Wiley & Sons, Inc.

Keywords: microarray analysis; gene functional annotation; bio‐databases; enrichment analysis; gene clustering

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: DAVID Gene List Management Panel: Submit and Manage User's Gene Lists in DAVID
  • Basic Protocol 2: DAVID Gene Name Batch Viewer: Explore Gene Names Based on User's Gene IDs
  • Basic Protocol 3: DAVID Gene Functional Classification Tool: Classify Users' Genes into Co‐Functional Gene Groups
  • Basic Protocol 4: DAVID Functional Annotation Tool: Identify Enriched Biology Within Users' Gene Lists
  • Basic Protocol 5: DAVID ID Conversion Tool: Convert Users' Gene IDs to Different Types
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Dennis, G. Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., and Lempicki, R.A. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4:P3.
   Huang, D.W., Sherman, B.T., Tan, Q., Collins, J.R., Alvord, W.G., Roayaei, J., Stephens, R., Baseler, M.W., Lane, H.C., and Lempicki, R.A. 2007a. The DAVID Gene Functional Classification Tool: A novel biological module‐centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R183.
   Huang, D.W., Sherman, B.T., Tan, Q., Kir, J., Liu, D., Bryant, D., Guo, Y., Stephens, R., Baseler, M.W., Lane, H.C., and Lempicki, R.A. 2007b. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35:W169‐W175.
   Huang, D.W., Sherman, B.T., Stephens, R., Baseler, M.W., Lane, H.C., and Lempicki, R.A. 2008. DAVID gene ID conversion tool. Bioinformation 2:428‐430.
   Huang, D.W., Sherman, B.T. and Lempicki, R.A. 2009. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37:1‐13.
   Sherman, B.T., Huang, D.W., Tan, Q., Guo, Y., Bour, S., Liu, D., Stephens, R., Baseler, M.W., Lane, H.C., and Lempicki, R.A. 2007. DAVID Knowledgebase: A gene‐centered database integrating heterogeneous gene annotation resources to facilitate high‐throughput gene functional analysis. BMC Bioinformatics 8:426.
Internet Resources
   http://david.abcc.ncifcrf.gov
  DAVID Bioinformatics Resources 2008.
   http://david.abcc.ncifcrf.gov/forum
  The DAVID Forum.
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