ArticlePLoS genetics2014
The functional consequences of variation in transcription factor binding.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed, 235 citations in OpenAlex.
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- The homeobox transcription factor MNX1 regulates the expression of many non-MN-specific neuronal genes in motor neurons.Nucleic acids research · 2025Article
- Combining Motifs, CRE Activity, And Gene Expression Data Using ML Greatly Improves the Accuracy of Tissue-Specific TF Network Maps.bioRxiv : the preprint server for biology · 2025Article
- Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.Evolutionary applications · 2025Article
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- The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA.EMBO reports · 2025Article
- Regulation of meristem and hormone function revealed through analysis of directly-regulated SHOOT MERISTEMLESS target genes.Scientific reports · 2025Article
- Binding profiles for 961Genome research · 2024Article
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- RummaGEO: Automatic mining of human and mouse gene sets from GEO.Patterns (New York, N.Y.) · 2024Article
- COFFEE: consensus single cell-type specific inference for gene regulatory networks.Briefings in bioinformatics · 2024Article
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- White-opaque switching inMicrobiology and molecular biology reviews : MMBR · 2024Review
- RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO.bioRxiv : the preprint server for biology · 2024Article
- A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network.Circulation · 2024Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. Using this approach, we found that only a small subset of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. We found that functional TF binding is enriched in regulatory elements that harbor a large number of TF binding sites, at sites with predicted higher binding affinity, and at sites that are enriched in genomic regions annotated as "active enhancers."
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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.