ArticleProceedings of the National Academy of Sciences of the United States of America2011
Cooperative transcription factor associations discovered using regulatory variation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed, 57 citations in OpenAlex.
- Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.bioRxiv : the preprint server for biology · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors.Nature communications · 2023Article
- RGS5 augments astrocyte activation and facilitates neuroinflammation via TNF signaling.Journal of neuroinflammation · 2023Article
- An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology.Cancers · 2022Article
- FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling.Nucleic acids research · 2022Article
- Genomic Analysis of Glioblastoma Multiforme Reveals a Key Transcription Factor Signature Relevant to Prognosis and the Immune Processes.Frontiers in oncology · 2021Article
- Effect for Human Genomic Variation During the BMP4-Induced Conversion From Pluripotent Stem Cells to Trophoblast.Frontiers in genetics · 2020Article
- Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding.Nature communications · 2019Article
- Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.BMC biology · 2019Article
- Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α.Nature communications · 2018Article
- Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.Genome research · 2017Article
- Evaluating the impact of single nucleotide variants on transcription factor binding.Nucleic acids research · 2016Article
- Article
- Prediction of fine-tuned promoter activity from DNA sequence.F1000Research · 2016Article
- A functional variant in miR-155 regulation region contributes to lung cancer risk and survival.Oncotarget · 2015Article
- Loregic: a method to characterize the cooperative logic of regulatory factors.PLoS computational biology · 2015Article
- Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.Nucleic acids research · 2014Article
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
Abstract
Regulation of gene expression at the transcriptional level is achieved by complex interactions of transcription factors operating at their target genes. Dissecting the specific combination of factors that bind each target is a significant challenge. Here, we describe in detail the Allele Binding Cooperativity test, which uses variation in transcription factor binding among individuals to discover combinations of factors and their targets. We developed the ALPHABIT (a large-scale process to hunt for allele binding interacting transcription factors) pipeline, which includes statistical analysis of binding sites followed by experimental validation, and demonstrate that this method predicts transcription factors that associate with NFκB. Our method successfully identifies factors that have been known to work with NFκB (E2A, STAT1, IRF2), but whose global coassociation and sites of cooperative action were not known. In addition, we identify a unique coassociation (EBF1) that had not been reported previously. We present a general approach for discovering combinatorial models of regulation and advance our understanding of the genetic basis of variation in transcription factor binding.
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.