RT Journal
A1 Walhout, Albertha J.M.
T1 Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
JF Genome Research 
JO Genome Research 
YR 2006 
FD December 01 
VO 16 
IS 12 
SP 1445 
OP 1454 
DO 10.1101/gr.5321506 
UL http://genome.cshlp.org/content/16/12/1445.abstract 
AB 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.