PharmGKB: An Integrated Resource of Pharmacogenomic Data and Knowledge

Li Gong1, Ryan P. Owen1, Winston Gor1, Russ B. Altman2, Teri E. Klein1

1 Genetics Department, Stanford University, Stanford, California, 2 Department of Bioengineering, Stanford University, Stanford, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.7
DOI:  10.1002/0471250953.bi1407s23
Online Posting Date:  September, 2008
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Abstract

The PharmGKB is a publicly available online resource that aims to facilitate understanding how genetic variation contributes to variation in drug response. It is not only a repository of pharmacogenomics primary data, but it also provides fully curated knowledge including drug pathways, annotated pharmacogene summaries, and relationships among genes, drugs, and diseases. This unit describes how to navigate the PharmGKB Web site to retrieve detailed information on genes and important variants, as well as their relationship to drugs and diseases. It also includes protocols on our drug‐centered pathway, annotated pharmacogene summaries, and our Web services for downloading the underlying data. Workflow on how to use PharmGKB to facilitate design of the pharmacogenomic study is also described in this unit. Curr. Protoc. Bioinform. 23:14.7.1‐14.7.17. © 2008 by John Wiley & Sons, Inc.

Keywords: database; pharmacogenomics; pharmacogenetics; drug response; genetic variation; pathway analysis; SNP; polymorphisms; study design

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Navigating the Homepage of PharmGKB Using Search by Gene
  • Support Protocol 1: Orientation to the PharmGKB Variant Page
  • Support Protocol 2: Orientation to the PharmGKB Pathway Pages
  • Support Protocol 3: Orientation to the VIP Gene Page
  • Support Protocol 4: Orientation to PharmGKB Web Services
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Literature Cited

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