ArticleNature protocols2011
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers, 5 of them syntheses that pooled it.
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Who cites it
159 citing papers in PubMed, 5 syntheses or guidelines pooled it, 250 citations in OpenAlex.
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- BAX -248 G>A and BCL2 -938 C>A Variant Lowers the Survival in Patients with Nasopharyngeal Carcinoma and Could be Associated with Tissue-Specific Malignancies: A Multi-Method Approach.Asian Pacific journal of cancer prevention : APJCP · 2021Pooled it
- Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer.Nature communications · 2018Pooled it
- Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error.Human molecular genetics · 2013Pooled it
- Meta-Analysis of Genome-Wide Association Studies of Doxorubicin-Induced Arrhythmia IdentifiesCirculation. Genomic and precision medicine · 2026Article
- FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.Nucleic acids research · 2026Article
- Pneumococcus uses COMMD2 to alter host cellular immunity.Nature communications · 2026Article
- Association of single nucleotide polymorphisms in FILIP1-SENP6 and FTO with temporomandibular joint osteoarthritis: clinical and in silico study.Scientific reports · 2026Article
- Integrative screening identifies functional variants and VNTRs underlying GWAS signals at the 5p15.33 multi-cancer susceptibility locus.medRxiv : the preprint server for health sciences · 2026Article
- Meta-analysis of genome-wide association studies of doxorubicin-induced arrhythmia identifiesmedRxiv : the preprint server for health sciences · 2025Article
- Cockayne syndrome mice reflect human kidney disease and are defective in de novo NAD biosynthesis.Cell death and differentiation · 2025Article
- Identification and functional characterization of an AMD associated c-ABL binding SNP streak within the ARMS2 gene promoter region.bioRxiv : the preprint server for biology · 2025Article
- Genomic diversity in Chinese Holstein cattle and genome-wide association study for body conformation traits.BMC genomics · 2025Article
- CFTR Gene Regulation in Human Pancreatic Duct, Bile Duct and Sweat Gland Epithelial Cells.Journal of cellular and molecular medicine · 2025Article
- Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5.Nature communications · 2025Article
- HMGA1 acts as an epigenetic gatekeeper of ASCL2 and Wnt signaling during colon tumorigenesis.The Journal of clinical investigation · 2025Article
- The interplay between hormonal vitamin D and lipopolysaccharide signaling on human neutrophil transcriptional responses.Frontiers in immunology · 2025Article
- ELK4 Promotes Vasculogenic Mimicry in Oral Squamous Cell Carcinoma via DrivingOncology research · 2025Article
- Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST.PloS one · 2025Article
99 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
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This protocol covers two other applications: (i) determining which transcription factors have the highest affinity in a set of sequences (illustrated with chromatin immunoprecipitation-sequencing (ChIP-seq) peaks), and (ii) finding which factor is the most affected by a regulatory single-nucleotide polymorphism. The protocol describes how to use the TRAP web tools to address these questions, and it also presents a way to run TRAP on random control sequences to better estimate the significance of the results. All of the tools are fully available online and do not need any additional installation. The complete protocol takes about 45 min, but each individual tool runs in a few minutes.
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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.