UMMS Affiliation

Program in Gene Function and Expression

Publication Date


Document Type



Animals; DNA-Binding Proteins; *Gene Expression Regulation; Genome; *Protein Interaction Mapping; Proteins; Regulatory Elements, Transcriptional; Regulatory Sequences, Nucleic Acid; Transcription Factors; *Transcription, Genetic


Life Sciences | Medicine and Health Sciences


Metazoan genomes contain thousands of protein-coding and noncoding RNA genes, most of which are differentially expressed, i.e., at different locations or at different times during development, function, or pathology of the organism. Differential gene expression is achieved in part by the action of regulatory transcription factors (TFs) that bind to cis-regulatory elements that are often located in or near their target genes. Each TF likely regulates many targets in the context of intricate transcription regulatory networks. Up to 10% of a genome may encode TFs, but only a handful of these have been studied in detail. Here, I will discuss the different steps involved in the mapping and analysis of transcription regulatory networks, including the identification of network nodes (TFs and their target sequences) and edges (TF-TF dimers and TF-DNA target interactions), integration with other data types, and network properties and emerging principles that provide insights into differential gene expression.

DOI of Published Version



Genome Res. 2006 Dec;16(12):1445-54. Epub 2006 Oct 19. Link to article on publisher's site

Journal/Book/Conference Title

Genome research

Related Resources

Link to Article in PubMed

PubMed ID