GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine
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(2020) 21:619
SOFTWARE
Open Access
GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine Guidantonio Malagoli Tagliazucchi1,2 and Cristian Taccioli3*
Abstract: Background: Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able to identify specific drugs at the level of single patient integrating multi-omics data such as RNA-sequencing, copynumber variation, methylation, Chromatin Immuno-Precipitation and Exome/Whole Genome sequencing. It is also possible to include clinical data related to each patient. GMIEC has been developed as a web-based R-Shiny platform and gives as output a table easy to use and explore. Results: We present GMIEC, a Shiny application for genomics medicine. The tool allows the users the integration of two or more multiple omics datasets (e.g. gene-expression, copy-number), at sample level, to identify groups of genes that share common genomic and corresponding drugs. We demonstrate the characteristics of our application by using it to analyze a prostate cancer data set. Conclusions: GMIEC provides a simple interface for genomics medicine. GMIEC was develop with Shiny to provide an application that does not require advanced programming skills. GMIEC consists of three sub-application for the analysis (GMIEC-AN), the visualization (GMIEC-VIS) and the exploration of results (GMIEC-RES). GMIEC is an open source software and is available at https://github.com/guidmt/GMIEC-shiny Keywords: Medical genomics, Precision medicine, Genomics, R, Shiny
Background More efficient drug therapies and better treatment are the promises of personalized medicine. In fact, precision medicine has created innovative opportunities to identify new drugs and therapeutic strategies. The integration of Next Generation Sequencing (NGS) data can be an important support to further tailor health care for each patient. Several methods of data fusion exist [1] and many tools were developed to integrate multiple genomic information [2–8]. However, these methods are not always straightforward because do not provide graphical * Correspondence: [email protected] 3 Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, PD, Italy Full list of author information is available at the end of the article
interfaces and the possibility to upload custom datasets. Moreover, it is not possible to search for group of genes (modules) with common molecular profiles as in GMIE C (Genomic Modules Identification et Characterization for genomics medicine). GMIEC is a flexible application that allows to integrate gene-expression, copy-number variation, methylation, Chromatin Immuno-Precipitation sequencing, mutations, and clinical data at the level of single patient. It analyses and, successively, links each mod
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