ArticleBioinformatics (Oxford, England)2021
Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3.Nucleic acids research · 2026Article
- Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification.Nature genetics · 2024Article
- Article
- CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes.Human genomics · 2023Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationGenome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of transcription factors (TFs) and therefore could alter gene expression. However, we currently lack a systematic understanding on how this mechanism contributes to phenotype.
resultsWe present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predictive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Given trait-associated non-coding variants, Motif-Raptor can recover relevant cell types and critical TFs to drive hypotheses regarding their mechanism of action. We tested Motif-Raptor on complex traits such as rheumatoid arthritis and red blood cell count and demonstrated its ability to prioritize relevant cell types, potential regulatory TFs and non-coding SNPs which have been previously characterized and validated. AVAILABILITY AND IMPLEMENTATION: Motif-Raptor is freely available as a Python package at: https://github.com/pinellolab/MotifRaptor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.