ArticleJournal of clinical bioinformatics2013
Plot protein: visualization of mutations.
Article in Journal of clinical bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Oral Phenotype of Singleton-Merten Syndrome: A Systematic Review Illustrated With a Case Report.Frontiers in genetics · 2022Pooled it
- Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection.Nature communications · 2018Trial
- MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation.Nature communications · 2026Article
- Whole Genome Sequencing Reveals amedRxiv : the preprint server for health sciences · 2026Article
- Proteome-wide assessment of differential missense variant clustering in neurodevelopmental disorders and cancer.Cell genomics · 2025Article
- Integrative structural analysis of NF45-NF90 heterodimers reveals architectural rearrangements and oligomerization on binding dsRNA.Nucleic acids research · 2025Article
- The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.EMBO reports · 2024Article
- Genetic variant profiling of neonatal diabetes mellitus in Iranian patients: Unveiling 58 distinct variants in 14 genes.Journal of diabetes investigation · 2024Article
- Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome.Life science alliance · 2023Article
- Neurofibromatosis-1 Gene Mutational Profiles Differ Between Syndromic Disease and Sporadic Cancers.Neurology. Genetics · 2022Article
- Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators.Journal of molecular biology · 2022Article
- Immunogenicity and Efficacy of a Recombinant Human Adenovirus Type 5 Vaccine against Zika Virus.Vaccines · 2020Article
- Mutplot: An easy-to-use online tool for plotting complex mutation data with flexibility.PloS one · 2019Article
- Article
- Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.Human molecular genetics · 2015Article
- Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing has enabled examination of variation at the DNA sequence level and can be further enhanced by evaluation of the variants at the protein level. One powerful method is to visualize these data often revealing patterns not immediately apparent in a text version of the same data. Many investigators are interested in knowing where their amino acid changes reside within a protein. Clustering of variation within a protein versus non-clustering can show interesting aspects of the biological changes happening in disease. FINDING: We describe a freely available tool, Plot Protein, executable from the command line or utilized as a graphical interface through a web browser, to enable visualization of amino acid changes at the protein level. This allows researchers to plot variation from their sequencing studies in a quick and uniform way. The features available include plotting amino acid changes, domains, post-translational modifications, reference sequence, conservation, conservation score, and also zoom capabilities. Herein we provide a case example using this tool to examine the RET protein and we demonstrate how clustering of mutations within the protein in Multiple Endocrine Neoplasia 2A (MEN2A) reveals important information about disease mechanism.
conclusionsPlot Protein is a useful tool for investigating amino acid changes and their localization within proteins. Command line and web server versions of this software are described that enable users to derive visual knowledge about their mutations.
Identifiers
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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.