Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes

Philippe Lamesch1, Kate Dreher1, David Swarbreck1, Rajkumar Sasidharan1, Leonore Reiser1, Eva Huala1

1 Carnegie Institution for Science, Stanford, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.11
DOI:  10.1002/0471250953.bi0111s30
Online Posting Date:  June, 2010
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Abstract

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, biochemical pathways, genome organization, images of mutant plants, protein sub‐cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web‐based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and describes several new tools such as a new TAIR genome browser (GBrowse), and the TAIR synteny viewer (GBrowse_syn). We also describe how to use AraCyc for mining plant metabolic pathways. Curr. Protoc. Bioinform. 30:1.11.1‐1.11.51. © 2010 by John Wiley & Sons, Inc.

Keywords: Arabidopsis; databases; bioinformatics; data mining; genomics

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: TAIR Homepage, Sitemap, and Navigation
  • Basic Protocol 2: Finding Comprehensive Information about Arabidopsis Genes
  • Basic Protocol 3: Using the Arabidopsis Genome Browsers (SeqViewer and GBrowse)
  • Basic Protocol 4: Using the Gene Ontology Annotations: Finding Genes with Similar Functions
  • Basic Protocol 5: Finding and Ordering Mutant Seeds and cDNA Clones from the Stock Center
  • Basic Protocol 6: Using Public Microarray Data in TAIR
  • Support Protocol 1: Mapping Array Elements to Annotated Loci
  • Basic Protocol 7: Using the Motif Analysis Tool for Identifying Potential cis‐Regulatory Motifs in Upstream Sequences
  • Basic Protocol 8: Obtaining Information about Arabidopsis Metabolic Pathways
  • Basic Protocol 9: Displaying Metabolic Data Using the “OMICS” Viewer
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Literature Cited

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