UMMS Affiliation

Program in Gene Function and Expression

Publication Date


Document Type



DNA; Genomics; Ligands; Protein Binding; Protein Processing, Post-Translational; Protein Structure, Tertiary; Transcription Factors; Transcription, Genetic


Life Sciences | Medicine and Health Sciences


Now that numerous high-quality complete genome sequences are available, many efforts are focusing on the "second genomic code", namely the code that determines how the precise temporal and spatial expression of each gene in the genome is achieved. In this regard, the elucidation of transcription regulatory networks that describe combined transcriptional circuits for an organism of interest has become valuable to our understanding of gene expression at a systems level. Such networks describe physical and regulatory interactions between transcription factors (TFs) and the target genes they regulate under different developmental, physiological, or pathological conditions. The mapping of high-quality transcription regulatory networks depends not only on the accuracy of the experimental or computational method chosen, but also relies on the quality of TF predictions. Moreover, the total repertoire of TFs is not only determined by the protein-coding capacity of the genome, but also by different protein properties, including dimerization, co-factor interactions and post-translational modifications. Here, we discuss the factors that influence TF functionality and, hence, the functionality of the networks in which they operate.

DOI of Published Version



Mol Biosyst. 2008 Apr;4(4):309-14. Epub 2008 Feb 21. Link to article on publisher's site

Journal/Book/Conference Title

Molecular bioSystems

Related Resources

Link to Article in PubMed

PubMed ID