UMMS Affiliation

Program in Systems Biology; Program in Molecular Medicine; UMass Metabolic Network

Publication Date


Document Type



Cellular and Molecular Physiology | Genetics | Genomics | Integrative Biology | Molecular Biology | Molecular Genetics | Systems Biology


Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene-centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two-thirds of which are novel, as well as integrate gene expression, protein-protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.


C. elegans, gene regulation, protein–DNA interaction network, transcription factors, yeast one‐hybrid assays

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Copyright 2016 The Authors.

DOI of Published Version



Mol Syst Biol. 2016 Oct 24;12(10):884. doi: 10.15252/msb.20167131.

Journal/Book/Conference Title

Molecular systems biology

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Link to Article in PubMed

PubMed ID


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.