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How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome

  • Juan M. VaquerizasEmail author
  • Sarah A. Teichmann
  • Nicholas M. Luscombe
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Abstract

Transcription factors (TFs) play an important role in regulating gene expression. The availability of complete genome sequences and associated functional genomic data offer excellent opportunities to understand the transcriptional regulatory system of an entire organism. To do so, however, it is essential to compile a reliable dataset of regulatory components. Here, we review computational methods and publicly accessible resources that help identify TF-coding genes in prokaryotic and eukaryotic genomes. Since the regulatory functions of most TFs remain unknown, we also discuss approaches for combining diverse genomic datasets that will help elucidate their chromosomal organisation, expression, and evolutionary conservation. These analysis methods provide a solid foundation for further investigations of the transcriptional regulatory system.

Key words

Transcription factor Genomics TF Transcriptional regulation Evolution Gene expression Genome organisation 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Juan M. Vaquerizas
    • 1
    Email author
  • Sarah A. Teichmann
    • 2
  • Nicholas M. Luscombe
    • 3
    • 4
  1. 1.EMBL-European Bioinformatics InstituteCambridgeUK
  2. 2.MRC Laboratory of Molecular BiologyCambridgeUK
  3. 3.EMBL-European Bioinformatics InstituteCambridgeUK
  4. 4.EMBL-Heidelberg Gene Expression UnitHeidelbergGermany

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