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

Leonore Reiser1, Shabari Subramaniam1, Donghui Li1, Eva Huala1

1 Phoenix Bioinformatics, Fremont, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.11
DOI:  10.1002/cpbi.36
Online Posting Date:  December, 2017
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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, orthologs, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, 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 genome. Additionally, we describe how members of the community can share data using TAIR's Online Annotation Submission Tool (TOAST), in order to make their published research more accessible and visible. © 2017 by John Wiley & Sons, Inc.

Keywords: Arabidopsis; bioinformatics; data mining; databases; 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 for Gene Discovery and Gene Function Analysis
  • Basic Protocol 5: Finding and Ordering Mutant Seeds and cDNA Clones from the Stock Center
  • Basic Protocol 6: Using Gene Lists to Download Bulk Datasets
  • Basic Protocol 7: Using TAIR's Analysis Tools to Find Short Sequences and Motifs
  • Basic Protocol 8: Using the TAIR Online Annotation Submission Tool (TOAST) to Submit Functional Annotations for Arabidopsis Genes
  • Basic Protocol 9: Using TAIR to Browse Arabidopsis Literature
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: TAIR Homepage, Sitemap, and Navigation

  Necessary Resources
  • See protocol 1

Basic Protocol 2: Finding Comprehensive Information About Arabidopsis Genes

  Necessary Resources
  • See protocol 1

Basic Protocol 3: Using the Arabidopsis Genome Browsers (SeqViewer and GBrowse)

  Necessary Resources
  • See protocol 1

Basic Protocol 4: Using the Gene Ontology Annotations for Gene Discovery and Gene Function Analysis

  Necessary Resources
  • See protocol 1

Basic Protocol 5: Finding and Ordering Mutant Seeds and cDNA Clones from the Stock Center

  Necessary Resources
  • See protocol 1

Basic Protocol 6: Using Gene Lists to Download Bulk Datasets

  Necessary Resources
  • See protocol 1

Basic Protocol 7: Using TAIR's Analysis Tools to Find Short Sequences and Motifs

  Necessary Resources
  • See protocol 1
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Figures

Videos

Literature Cited

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