ArticleCell reports2017
Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity.
Article in Cell reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
What it found
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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.
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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.
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Who cites it
78 citing papers in PubMed, 135 citations in OpenAlex.
- Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.Molecular systems biology · 2026Article
- Aberrant splicing in human cancer shows possible functional impact on transcription factors.Oncogene · 2026Article
- Glis3 Is a Modifier of Cyst Progression in Autosomal Dominant Polycystic Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Article
- SIRT6 overexpression counteracts chromatin aging in the male murine liver.Nature communications · 2026Article
- Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation.bioRxiv : the preprint server for biology · 2026Article
- CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline.EMBO molecular medicine · 2026Article
- Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease.Science advances · 2025Article
- Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles.bioRxiv : the preprint server for biology · 2025Article
- Mutation of CHD7 impairs the output of neuroepithelium transition that is reversed by the inhibition of EZH2.Molecular psychiatry · 2025Article
- Molecular Determinants of the Human Retinal Pigment Epithelium Cell Fate and Potential Pharmacogenomic Targets for Precision Medicine.International journal of molecular sciences · 2025Article
- Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- Repeated fasting events sensitize enhancers, transcription factor activity and gene expression to support augmented ketogenesis.Nucleic acids research · 2025Article
- ATAC-seq for Characterizing Host and Pathogen Genome Accessibility During Virus Infection.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- On the identification of differentially-active transcription factors from ATAC-seq data.PLoS computational biology · 2024Article
- LXR-dependent enhancer activation regulates the temporal organization of the liver's response to refeeding leading to lipogenic gene overshoot.PLoS biology · 2024Article
- Cellular zinc status alters chromatin accessibility and binding of p53 to DNA.Life science alliance · 2024Article
- On the identification of differentially-active transcription factors from ATAC-seq data.bioRxiv : the preprint server for biology · 2024Article
- Optimized reporters for multiplexed detection of transcription factor activity.bioRxiv : the preprint server for biology · 2024Article
18 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
3 authors at 1 institution in 1 country.
Funding
Abstract
In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility. The algorithm, termed bivariate genomic footprinting (BaGFoot), efficiently detects TF activity. BaGFoot is robust to different accessibility assays (DNase-seq, ATAC-seq), all examined peak-calling programs, and a variety of cut bias correction approaches. BaGFoot reliably predicts TF binding and provides valuable information regarding the TFs affecting chromatin accessibility in various biological systems and following various biological events, including in cases where an absolute footprint cannot be determined.
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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.