ArticleMolecular systems biology2016
A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.
Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 78 citations in OpenAlex.
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- RNA methyltransferase CMTR-1 inhibition activates a GATA transcription factor-mediated protective immune response.bioRxiv : the preprint server for biology · 2025Article
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- Molecular profiling of adult C. elegans glia across sexes by single-nuclear RNA-seq.Developmental cell · 2025Article
- An updated compendium of Caenorhabditis elegans RNA-binding proteins and their regulation.G3 (Bethesda, Md.) · 2025Article
- Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.Nature communications · 2025Article
- Repeated Evolution of Transcript Dosage Compensation of Independently Formed Nematode Neo-X Chromosomes.Genome biology and evolution · 2025Article
- CelEst: a unified gene regulatory network for estimating transcription factor activities in C. elegans.Genetics · 2025Article
- Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.bioRxiv : the preprint server for biology · 2025Article
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- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.Nucleic acids research · 2024Article
- A double-negative feedback loop between miR319c and JAW-TCPs establishes growth pattern in incipient leaf primordia in Arabidopsis thaliana.PLoS genetics · 2023Article
- Transcript accumulation rates in the earlyScience advances · 2023Article
- Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.