Author | Pires, Jorge Guerra | |
Author | Silva, Gilberto Ferreira da | |
Author | Weyssow, Thomas | |
Author | Conforte, Alessandra Jordano | |
Author | Pagnoncelli, Dante | |
Author | Silva, Fabrício Alves Barbosa da | |
Author | Carels, Nicolas | |
Access date | 2023-07-13T23:49:14Z | |
Available date | 2023-07-13T23:49:14Z | |
Document date | 2021 | |
Citation | PIRES, Jorge Guerra et al. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Frontiers in Genetics, Switzerland, v. 12, p. 1-26, Feb. 2021. | en_US |
ISSN | 1664-8021 | en_US |
URI | https://www.arca.fiocruz.br/handle/icict/59580 | |
Language | eng | en_US |
Publisher | Frontiers Media S.A. | en_US |
Rights | open access | en_US |
Title | Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy | en_US |
Type | Article | en_US |
DOI | 10.3389/FGENE.2021.624259 | |
Abstract | One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection <i>hubs</i> in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis <i>in vitro</i>. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries. | en_US |
Affilliation | Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Informatic Department. Free University of Brussels (ULB). Brussels, Belgium. | en_US |
Affilliation | Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil / Oswaldo Cruz Foundation. Presidency. Scientific Computing Program. Laboratório de Modelagem Computacional de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Instituto COI. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Oswaldo Cruz Foundation. Presidency. Scientific Computing Program. Laboratório de Modelagem Computacional de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil. | en_US |
Affilliation | Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil. | en_US |
Subject | Systems biology | en_US |
Subject | Translational oncology | en_US |
Subject | Personalized medicine | en_US |
Subject | Galaxy | en_US |
Subject | MEAN stack | en_US |
Subject | Angular | en_US |
Subject | Protein–protein network | en_US |
Subject | Shannon entropy | en_US |
e-ISSN | 1664-8021 | |