Gene Regulatory Networks

Volume 786 of the series Methods in Molecular Biology pp 3-19


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

  • Juan M. VaquerizasAffiliated withEMBL-European Bioinformatics Institute Email author 
  • , Sarah A. TeichmannAffiliated withMRC Laboratory of Molecular Biology
  • , Nicholas M. LuscombeAffiliated withEMBL-European Bioinformatics InstituteEMBL-Heidelberg Gene Expression Unit

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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