Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

Abstract Toxygates was originally released as a user-friendly interface to enhance the accessibility of the large-scale toxicogenomics database, Open TG-GATEs, generated by the Japanese Toxicogenomics Project. Since the original release, significant new functionality has been added to enable users t...

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Autores principales:	Johan Nyström-Persson, Yayoi Natsume-Kitatani, Yoshinobu Igarashi, Daisuke Satoh, Kenji Mizuguchi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1884fb74a1b94882b11cd136fbe69ccf
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spelling	oai:doaj.org-article:1884fb74a1b94882b11cd136fbe69ccf2021-12-02T16:06:51ZInteractive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates10.1038/s41598-017-01500-12045-2322https://doaj.org/article/1884fb74a1b94882b11cd136fbe69ccf2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01500-1https://doaj.org/toc/2045-2322Abstract Toxygates was originally released as a user-friendly interface to enhance the accessibility of the large-scale toxicogenomics database, Open TG-GATEs, generated by the Japanese Toxicogenomics Project. Since the original release, significant new functionality has been added to enable users to perform sophisticated computational analysis with only modest bioinformatics skills. The new features include an orthologous mode for data comparison among different species, interactive clustering and heatmap visualisation, enrichment analysis of gene sets, and user data uploading. In a case study, we use these new functions to study the hepatotoxicity of peroxisome proliferator-activated receptor alpha (PPARα) agonist WY-14643. Our findings suggest that WY-14643 caused hypertrophy in the bile duct by intracellular Ca2+ dysregulation, which resulted in the induction of genes in a non-canonical WNT/Ca2+ signalling pathway. With this new release of Toxygates, we provide a suite of tools that allow anyone to carry out in-depth analysis of toxicogenomics in Open TG-GATEs, and of any other dataset that is uploaded.Johan Nyström-PerssonYayoi Natsume-KitataniYoshinobu IgarashiDaisuke SatohKenji MizuguchiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Johan Nyström-Persson Yayoi Natsume-Kitatani Yoshinobu Igarashi Daisuke Satoh Kenji Mizuguchi Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
description	Abstract Toxygates was originally released as a user-friendly interface to enhance the accessibility of the large-scale toxicogenomics database, Open TG-GATEs, generated by the Japanese Toxicogenomics Project. Since the original release, significant new functionality has been added to enable users to perform sophisticated computational analysis with only modest bioinformatics skills. The new features include an orthologous mode for data comparison among different species, interactive clustering and heatmap visualisation, enrichment analysis of gene sets, and user data uploading. In a case study, we use these new functions to study the hepatotoxicity of peroxisome proliferator-activated receptor alpha (PPARα) agonist WY-14643. Our findings suggest that WY-14643 caused hypertrophy in the bile duct by intracellular Ca2+ dysregulation, which resulted in the induction of genes in a non-canonical WNT/Ca2+ signalling pathway. With this new release of Toxygates, we provide a suite of tools that allow anyone to carry out in-depth analysis of toxicogenomics in Open TG-GATEs, and of any other dataset that is uploaded.
format	article
author	Johan Nyström-Persson Yayoi Natsume-Kitatani Yoshinobu Igarashi Daisuke Satoh Kenji Mizuguchi
author_facet	Johan Nyström-Persson Yayoi Natsume-Kitatani Yoshinobu Igarashi Daisuke Satoh Kenji Mizuguchi
author_sort	Johan Nyström-Persson
title	Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
title_short	Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
title_full	Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
title_fullStr	Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
title_full_unstemmed	Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
title_sort	interactive toxicogenomics: gene set discovery, clustering and analysis in toxygates
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/1884fb74a1b94882b11cd136fbe69ccf
work_keys_str_mv	AT johannystrompersson interactivetoxicogenomicsgenesetdiscoveryclusteringandanalysisintoxygates AT yayoinatsumekitatani interactivetoxicogenomicsgenesetdiscoveryclusteringandanalysisintoxygates AT yoshinobuigarashi interactivetoxicogenomicsgenesetdiscoveryclusteringandanalysisintoxygates AT daisukesatoh interactivetoxicogenomicsgenesetdiscoveryclusteringandanalysisintoxygates AT kenjimizuguchi interactivetoxicogenomicsgenesetdiscoveryclusteringandanalysisintoxygates
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Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

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