ArticleGenome biology2017
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.Genome biology · 2026Article
- Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry.Nature communications · 2025Article
- Epistatic contributions to human traits via transcription factor mechanisms.medRxiv : the preprint server for health sciences · 2025Article
- Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis.Nature communications · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro.Arteriosclerosis, thrombosis, and vascular biology · 2024Article
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- Article
- Deletion in a regulatory region is associated with underexpression of miR-148b‑3p in patients with prostate cancer.Biomedical reports · 2024Article
- Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs.BMC bioinformatics · 2023Article
- De novo human brain enhancers created by single-nucleotide mutations.Science advances · 2023Article
- ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.Nucleic acids research · 2022Article
- Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning.Genome research · 2021Article
- Landscape of allele-specific transcription factor binding in the human genome.Nature communications · 2021Article
- Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.International journal of molecular sciences · 2021Review
- Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease.American journal of human genetics · 2021Article
- regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data.Frontiers in bioengineering and biotechnology · 2020Article
- Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells.Immunity · 2019Article
- An empirical Bayes test for allelic-imbalance detection in ChIP-seq.Biostatistics (Oxford, England) · 2018Article
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Authors and funding
8 authors.
Funding
Abstract
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and six targeted FAIRE-seq samples, we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.
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