BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
نویسندگان
چکیده
منابع مشابه
Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding
A causative role for single nucleotide polymorphisms (SNPs) in many genetic disorders has become evident through numerous genome-wide association studies. However, identification of these common causal variants and the molecular mechanisms underlying these associations remains a major challenge. Differential transcription factor binding at a SNP resulting in altered gene expression is one possi...
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Aneuploidy and structural variations (SVs) generate cancer genomes containing a mixture of rearranged genomic segments with extensive somatic copy number alterations. However, existing methods can identify either SVs or allele-specific copy number alterations but not both simultaneously, which provides a limited view of cancer genome structure. Here, we introduce Weaver, an algorithm for the qu...
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Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is called a motif. Several recent studies of transcriptional regulation require the reduction of a large collection of motifs into clusters based on the similar...
متن کاملPhylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using...
متن کاملAllelic imbalance assays to quantify allele-specific gene expression and transcription factor binding.
A growing number of noncoding variants are found to influence the susceptibility to common diseases and interindividual variation in drug response. However, the mechanisms by which noncoding variation affects cellular and clinical phenotypes remain to be elucidated. Allele-specific assays allow testing directly the differential properties of the alleles at a regulatory variant, which are detect...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2017
ISSN: 1474-760X
DOI: 10.1186/s13059-017-1165-7