ArticleScientific reports2015
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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
28 citing papers in PubMed, 49 citations in OpenAlex.
- Long-range transcription factor binding sites clustered regions may mediate transcriptional regulation through phase-separation interactions in early human embryo.Computational and structural biotechnology journal · 2024Article
- The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.Nucleic acids research · 2024Article
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.Briefings in bioinformatics · 2024Article
- MMGAT: a graph attention network framework for ATAC-seq motifs finding.BMC bioinformatics · 2024Article
- CLIC3 interacts with NAT10 to inhibit N4-acetylcytidine modification of p21 mRNA and promote bladder cancer progression.Cell death & disease · 2024Article
- Identification of transcription factor high accumulation DNA zones.BMC bioinformatics · 2023Article
- Nucleotide alterations in the HLA-C class I gene can cause aberrant splicing and marked changes in RNA levels in a polymorphic context-dependent manner.Frontiers in immunology · 2023Article
- Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.Briefings in bioinformatics · 2022Article
- Article
- Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer.Computational and structural biotechnology journal · 2022Article
- Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals.Computational and structural biotechnology journal · 2022Article
- Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits.BMC genomics · 2021Article
- Mechanisms of enhancer action: the known and the unknown.Genome biology · 2021Review
- Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model.Scientific reports · 2021Article
- Intronic regions of theHeliyon · 2020Article
- MYCN is amplified during S phase, and c‑myb is involved in controlling MYCN expression and amplification in MYCN‑amplified neuroblastoma cell lines.Molecular medicine reports · 2019Article
- Borders ofFrontiers in genetics · 2018Article
- Exploring spatially adjacent TFBS-clustered regions with Hi-C data.Bioinformatics (Oxford, England) · 2017Article
- Identification of introns harboring functional sequence elements through positional conservation.Scientific reports · 2017Article
- RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNase I hypersensitive sites (DHSs) define the accessible chromatin landscape and have revolutionised the discovery of distinct cis-regulatory elements in diverse organisms. Here, we report the first comprehensive map of human transcription factor binding site (TFBS)-clustered regions using Gaussian kernel density estimation based on genome-wide mapping of the TFBSs in 133 human cell and tissue types. Approximately 1.6 million distinct TFBS-clustered regions, collectively spanning 27.7% of the human genome, were discovered. The TFBS complexity assigned to each TFBS-clustered region was highly correlated with genomic location, cell selectivity, evolutionary conservation, sequence features, and functional roles. An integrative analysis of these regions using ENCODE data revealed transcription factor occupancy, transcriptional activity, histone modification, DNA methylation, and chromatin structures that varied based on TFBS complexity. Furthermore, we found that we could recreate lineage-branching relationships by simple clustering of the TFBS-clustered regions from terminally differentiated cells. Based on these findings, a model of transcriptional regulation determined by TFBS complexity is proposed.
Indexed as
Identifiers
What OpenQuestion holds
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.