ArticleScientific reports2021
Mutational processes in cancer preferentially affect binding of particular transcription factors.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 7 citations in OpenAlex.
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Nature communications · 2026Article
- Biochemical, structural and mutational landscapes of base excision repair enzymes and cancer: from atomic resolution to tumor signatures.International journal of radiation biology · 2026Review
- KGLAR: Deconvoluting Spatial Transcriptomics Data with Single-cell Transcriptomes through Knowledge-guided NMF and Least Angle Regression.Interdisciplinary sciences, computational life sciences · 2026Article
- IRDRM: Exploring Biological Traits and Clinical Significance in Breast Cancer Through Gene Pairs and Somatic Mutation Profiles.Interdisciplinary sciences, computational life sciences · 2026Article
- HRD-Informed Digital Histology Model for Predicting Platinum Chemo-Response and Prognosis in High-Grade Serous Ovarian Cancer.Interdisciplinary sciences, computational life sciences · 2026Article
- ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis.Interdisciplinary sciences, computational life sciences · 2025Article
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Research square · 2025Article
- Comprehensive Mutational Landscape of Yeast Mutator Strains Reveals the Genetic Basis of Mutational Signatures in Cancer.Molecular biology and evolution · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Direct observation of DNA alterations induced by a DNA disruptor.Scientific reports · 2022Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Protein binding microarrays provide comprehensive information about the DNA binding specificities of transcription factors (TFs), and can be used to quantitatively predict the effects of DNA sequence variation on TF binding. There has also been substantial progress in dissecting the patterns of mutations, i.e., the "mutational signatures", generated by different mutational processes. By combining these two layers of information we can investigate whether certain mutational processes tend to preferentially affect binding of particular classes of TFs. Such preferential alterations of binding might predispose to particular oncogenic pathways. We developed and implemented a method, termed "Signature-QBiC", that integrates protein binding microarray data with the signatures of mutational processes, with the aim of predicting which TFs' binding profiles are preferentially perturbed by particular mutational processes. We used Signature-QBiC to predict the effects of 47 signatures of mutational processes on 582 human TFs. Pathway analysis showed that binding of TFs involved in NOTCH1 signaling is strongly affected by the signatures of several mutational processes, including exposure to ultraviolet radiation. Additionally, toll-like-receptor signaling pathways are also vulnerable to disruption by this exposure. This study provides a novel overview of the effects of mutational processes on TF binding and the potential of these processes to activate oncogenic pathways through mutating TF binding sites.
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