ReviewTrends in genetics : TIG2011
Genome-wide transcription factor binding: beyond direct target regulation.
Review in Trends in genetics : TIG, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it.
- XRCC1 polymorphisms and cervical cancer risk: an updated meta-analysis.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Pooled it
- KLF18 is a necessary component of the DUX4-initiated transcriptional network and a candidate locus for phenotypic diversity.Genes & development · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Lentivirus-Mediated Measurement of Transcription Factor Activity in the Brain.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage.Genes & development · 2025Article
- Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome.bioRxiv : the preprint server for biology · 2025Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- TExCNN: Leveraging Pre-Trained Models to Predict Gene Expression from Genomic Sequences.Genes · 2024Article
- A MOZ-TIF2 leukemia mouse model displays KAT6-dependent H3K23 propionylation and overexpression of a set of active developmental genes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states.bioRxiv : the preprint server for biology · 2024Article
- PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data.Frontiers in genetics · 2024Article
- Article
- KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.Scientific reports · 2023Article
- Building High-Confidence Gene Regulatory Networks by Integrating Validated TF-Target Gene Interactions Using ConnecTF.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Multi-Layered Regulations on the Chromatin Architectures: Establishing the Tight and Specific Responses of Fission YeastBiomolecules · 2022Review
- Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer.Science advances · 2022Article
- Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands.BMC genomics · 2022Article
- Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis.Arthritis & rheumatology (Hoboken, N.J.) · 2021Article
- Reciprocal stabilization of transcription factor binding integrates two signaling pathways to regulate fission yeast fbp1 transcription.Nucleic acids research · 2021Article
72 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The binding of transcription factors to specific DNA target sequences is the fundamental basis of gene regulatory networks. Chromatin immunoprecipitation combined with DNA tiling arrays or high-throughput sequencing (ChIP-chip and ChIP-seq, respectively) has been used in many recent studies that detail the binding sites of various transcription factors. Surprisingly, data from a variety of model organisms and tissues have demonstrated that transcription factors vary greatly in their number of genomic binding sites, and that binding events can significantly exceed the number of known or possible direct gene targets. Thus, current understanding of transcription factor function must expand to encompass what role, if any, binding might have outside of direct transcriptional target regulation. In this review, we discuss the biological significance of genome-wide binding of transcription factors and present models that can account for this phenomenon.
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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.