ArticleGenome research2020
Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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
20 citing papers in PubMed.
- CTCF-FXN regulatory axis plays critical roles in clinical assessments and disease progression of primary open-angle glaucoma.Journal of molecular medicine (Berlin, Germany) · 2026Article
- UBIQUITOUS FUNCTIONAL SYNERGY PARTIALLY EXPLAINS WHY MOST TRANSCRIPTION FACTOR BINDING IS NON-FUNCTIONAL.bioRxiv : the preprint server for biology · 2026Article
- Article
- Combining Motifs, CRE Activity, And Gene Expression Data Using ML Greatly Improves the Accuracy of Tissue-Specific TF Network Maps.bioRxiv : the preprint server for biology · 2025Article
- Mapping the transcriptional regulatory network of a fungal pathogen by exploiting transcription factor perturbation.bioRxiv : the preprint server for biology · 2025Article
- Article
- Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.PLoS computational biology · 2025Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Associations of differentially expressed genes with psychoneurological symptoms in patients with head and neck cancer: A longitudinal study.Journal of psychosomatic research · 2023Article
- FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.PLoS computational biology · 2023Article
- Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli.Nature communications · 2023Article
- The beneficial effects of chick embryo extract preconditioning on hair follicle stem cells: A promising strategy to generate Schwann cells.Cell proliferation · 2023Article
- Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.Nucleic acids research · 2023Article
- Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets.Genome research · 2023Article
- NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration.Bioinformatics (Oxford, England) · 2023Article
- Predicting which genes will respond to transcription factor perturbations.G3 (Bethesda, Md.) · 2022Article
- Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.Bioinformatics (Oxford, England) · 2021Article
- A genome-scale yeast library with inducible expression of individual genes.Molecular systems biology · 2021Article
- Article
- Learning causal networks using inducible transcription factors and transcriptome-wide time series.Molecular systems biology · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
A high-confidence map of the direct, functional targets of each transcription factor (TF) requires convergent evidence from independent sources. Two significant sources of evidence are TF binding locations and the transcriptional responses to direct TF perturbations. Systematic data sets of both types exist for yeast and human, but they rarely converge on a common set of direct, functional targets for a TF. Even the few genes that are both bound and responsive may not be direct functional targets. Our analysis shows that when there are many nonfunctional binding sites and many indirect targets, nonfunctional sites are expected to occur in the
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Registered trials
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