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shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations
While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to th...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802933/ https://www.ncbi.nlm.nih.gov/pubmed/29415010 http://dx.doi.org/10.1371/journal.pone.0192563 |
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author | Dwivedi, Bhakti Kowalski, Jeanne |
author_facet | Dwivedi, Bhakti Kowalski, Jeanne |
author_sort | Dwivedi, Bhakti |
collection | PubMed |
description | While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/. |
format | Online Article Text |
id | pubmed-5802933 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-58029332018-02-23 shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations Dwivedi, Bhakti Kowalski, Jeanne PLoS One Research Article While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/. Public Library of Science 2018-02-07 /pmc/articles/PMC5802933/ /pubmed/29415010 http://dx.doi.org/10.1371/journal.pone.0192563 Text en © 2018 Dwivedi, Kowalski http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Dwivedi, Bhakti Kowalski, Jeanne shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title | shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title_full | shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title_fullStr | shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title_full_unstemmed | shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title_short | shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations |
title_sort | shinygispa: a web application for characterizing phenotype by gene sets using multiple omics data combinations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802933/ https://www.ncbi.nlm.nih.gov/pubmed/29415010 http://dx.doi.org/10.1371/journal.pone.0192563 |
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