Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs

• Published in: BMC bioinformatics Vol. 24; no. 1; p. 464
• Main Authors: Li, Ying, Zhang, Xiao-Ou, Liu, Yan, Lu, Aiping
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 08.12.2023; BioMed Central; BMC
• Subjects: Algorithms; Allele-specific binding; Alleles; Analysis; Annotations; Bias; Binding; Binding Sites; Binomial distribution; Chromosomes; Cytogenetics; DNA binding proteins; Genetic aspects; Genomes; Genotype & phenotype; Health risks; Hypotheses; Hypothesis testing; Motif analysis; Nucleotides; Phenotypes; Polymorphism; Polymorphism, Single Nucleotide; Protein Binding; Single nucleotide polymorphism; Single nucleotide polymorphisms; Software; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; China; Allele-specific binding; Single nucleotide polymorphism; Motif analysis
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05604-6

Allele-specific binding (ASB) events occur when transcription factors (TFs) bind more favorably to one of the two parental alleles at heterozygous single nucleotide polymorphisms (SNPs). Evidence suggests that ASB events could reveal the impact of sequence variations on TF binding and may have implications for the risk of diseases. Here we present ASB-analyzer, a software platform that enables the users to quickly and efficiently input raw sequencing data to generate individual reports containing the cytogenetic map of ASB SNPs and their associated phenotypes. This interactive tool thereby combines ASB SNP identification, biological annotation, motif analysis, phenotype associations and report summary in one pipeline. With this pipeline, we identified 3772 ASB SNPs from thirty GM12878 ChIP-seq datasets and demonstrated that the ASB SNPs were more likely to be enriched at important sites in TF-binding domains. ASB-analyzer is a user-friendly tool that enables the detection, characterization and visualization of ASB SNPs. It is implemented in Python, R and bash shell and packaged in the Conda environment. It is available as an open-source tool on GitHub at https://github.com/Liying1996/ASBanalyzer .