ArticleBMC bioinformatics2016
MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A practical framework RNMF for exploring the association between mutational signatures and genes using gene cumulative contribution abundance.Cancer medicine · 2022Pooled it
- Integrating liquid biopsy and mutational signatures to advance precision oncology.NPJ precision oncology · 2026Review
- Evaluating topography of mutational signatures with SigProfilerTopography.Genome biology · 2025Article
- A review on trends in development and translation of omics signatures in cancer.Computational and structural biotechnology journal · 2024Review
- MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification.Bioinformatics (Oxford, England) · 2024Article
- Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications.Cancers · 2023Review
- Uncovering novel mutational signatures byCell genomics · 2022Article
- Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine.Briefings in bioinformatics · 2022Review
- Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure.International journal of cancer · 2022Article
- Accuracy of mutational signature software on correlated signatures.Scientific reports · 2022Article
- Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures.DNA repair · 2021Review
- Article
- Whole Genome Sequencing of the Mutamouse Model Reveals Strain- and Colony-Level Variation, and Genomic Features of the Transgene Integration Site.Scientific reports · 2019Article
- Integrated analyses of murine breast cancer models reveal critical parallels with human disease.Nature communications · 2019Article
- Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans.Genome research · 2019Article
- Computational approaches for discovery of mutational signatures in cancer.Briefings in bioinformatics · 2019Review
- Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance.PloS one · 2019Review
- Molecular features of premenopausal breast cancers in Latin American women: Pilot results from the PRECAMA study.PloS one · 2019Article
- Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets.BMC genomics · 2018Article
- Mutational signatures and mutable motifs in cancer genomes.Briefings in bioinformatics · 2018Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundThe nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called MutSpec.
resultsMutSpec includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the COSMIC database and other sources. MutSpec offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. MutSpec may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool.
conclusionsMutSpec offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. MutSpec can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.
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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.