ArticleBMC bioinformatics2013
Flanking sequence context-dependent transcription factor binding in early Drosophila development.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
- TF paralogs-Natural experiments in DNA binding.Current opinion in structural biology · 2025Review
- Article
- Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data.Briefings in bioinformatics · 2025Article
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- A comprehensive map of preferentially located motifs reveals distinct proximalFrontiers in plant science · 2022Article
- A k-mer grammar analysis to uncover maize regulatory architecture.BMC plant biology · 2019Article
- Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria.Nucleic acids research · 2018Article
- Article
- Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.Mechanisms of development · 2016Article
- Quantitative modeling of gene expression using DNA shape features of binding sites.Nucleic acids research · 2016Article
- Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome.Gene regulation and systems biology · 2016Article
- MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundGene expression in the Drosophila embryo is controlled by functional interactions between a large network of protein transcription factors (TFs) and specific sequences in DNA cis-regulatory modules (CRMs). The binding site sequences for any TF can be experimentally determined and represented in a position weight matrix (PWM). PWMs can then be used to predict the location of TF binding sites in other regions of the genome, although there are limitations to this approach as currently implemented.
resultsIn this proof-of-principle study, we analyze 127 CRMs and focus on four TFs that control transcription of target genes along the anterio-posterior axis of the embryo early in development. For all four of these TFs, there is some degree of conserved flanking sequence that extends beyond the predicted binding regions. A potential role for these conserved flanking sequences may be to enhance the specificity of TF binding, as the abundance of these sequences is greatly diminished when we examine only predicted high-affinity binding sites.
conclusionsExpanding PWMs to include sequence context-dependence will increase the information content in PWMs and facilitate a more efficient functional identification and dissection of CRMs.
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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.