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The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization

BACKGROUND: Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental bi...

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Autores principales: Li, Yin, Ge, Di, Lu, Chunlai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894252/
https://www.ncbi.nlm.nih.gov/pubmed/31805986
http://dx.doi.org/10.1186/s13072-019-0316-3
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author Li, Yin
Ge, Di
Lu, Chunlai
author_facet Li, Yin
Ge, Di
Lu, Chunlai
author_sort Li, Yin
collection PubMed
description BACKGROUND: Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. RESULTS: To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project. The SMART App integrates multi-omics and clinical data with DNA methylation and provides key interactive and customized functions including CpG visualization, pan-cancer methylation profile, differential methylation analysis, correlation analysis and survival analysis for users to analyze the DNA methylation in diverse cancer types in a multi-dimensional manner. CONCLUSION: The SMART App serves as a new approach for users, especially wet-bench scientists with no programming background, to analyze the scientific big data and facilitate data mining. The SMART App is available at http://www.bioinfo-zs.com/smartapp.
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spelling pubmed-68942522019-12-11 The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization Li, Yin Ge, Di Lu, Chunlai Epigenetics Chromatin Methodology BACKGROUND: Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. RESULTS: To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project. The SMART App integrates multi-omics and clinical data with DNA methylation and provides key interactive and customized functions including CpG visualization, pan-cancer methylation profile, differential methylation analysis, correlation analysis and survival analysis for users to analyze the DNA methylation in diverse cancer types in a multi-dimensional manner. CONCLUSION: The SMART App serves as a new approach for users, especially wet-bench scientists with no programming background, to analyze the scientific big data and facilitate data mining. The SMART App is available at http://www.bioinfo-zs.com/smartapp. BioMed Central 2019-12-05 /pmc/articles/PMC6894252/ /pubmed/31805986 http://dx.doi.org/10.1186/s13072-019-0316-3 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology
Li, Yin
Ge, Di
Lu, Chunlai
The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title_full The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title_fullStr The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title_full_unstemmed The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title_short The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
title_sort smart app: an interactive web application for comprehensive dna methylation analysis and visualization
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894252/
https://www.ncbi.nlm.nih.gov/pubmed/31805986
http://dx.doi.org/10.1186/s13072-019-0316-3
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