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gene‐centered regulatory networks
Author(s) -
Walhout Marian
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.314.1
Subject(s) - gene , biology , computational biology , gene regulatory network , encode , genetics , genome , transcription factor , regulatory sequence , regulation of gene expression , dna binding site , function (biology) , gene expression , promoter
The expression of each of our ~25,000 genes in different tissues or under different conditions is critical for our proper development and function. Indeed, changes in gene expression caused by mutations in transcription factors (TFs) or the cis‐regulatory genomic DNA elements they bind to (TF binding sites, or TFBSs) can result in a variety of human diseases. In order to fully understand development and pathologies, and to design effective therapeutics it is critical to understand which TF regulates the expression of which gene, where and under which conditions. In addition, it is essential to know the elements each TF binds to and where in the genome these TFBSs are located. This is a major challenge in genomic science as very little is known about the targets, binding sites, transcriptional activity and biological function for the majority of metazoan TFs. We use the nematode C. elegans to address this challenge. The C. elegans genome contains ~20,000 protein‐coding genes, 940 of which we predict encode regulatory TFs. We use gene‐centered, rather than TF‐centered (e.g. ChIP), protein‐DNA interaction mapping methods to map gene regulatory networks. We then integrate these networks with other networks and data types and analyze how regulatory networks and their properties relate to healthy as well as pathological system states. Progress on network mapping and characterization will be discussed.