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DNA microarray integromics analysis platform

BACKGROUND: The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computa...

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Autores principales: Waller, Tomasz, Gubała, Tomasz, Sarapata, Krzysztof, Piwowar, Monika, Jurkowski, Wiktor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479227/
https://www.ncbi.nlm.nih.gov/pubmed/26110022
http://dx.doi.org/10.1186/s13040-015-0052-6
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author Waller, Tomasz
Gubała, Tomasz
Sarapata, Krzysztof
Piwowar, Monika
Jurkowski, Wiktor
author_facet Waller, Tomasz
Gubała, Tomasz
Sarapata, Krzysztof
Piwowar, Monika
Jurkowski, Wiktor
author_sort Waller, Tomasz
collection PubMed
description BACKGROUND: The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of “multi-omics” data. Our tool supports a range of complex analyses, including – among others – low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions. RESULTS: We demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses. CONCLUSIONS: The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for “multi-omics” data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.
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spelling pubmed-44792272015-06-25 DNA microarray integromics analysis platform Waller, Tomasz Gubała, Tomasz Sarapata, Krzysztof Piwowar, Monika Jurkowski, Wiktor BioData Min Software Article BACKGROUND: The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of “multi-omics” data. Our tool supports a range of complex analyses, including – among others – low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions. RESULTS: We demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses. CONCLUSIONS: The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for “multi-omics” data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/. BioMed Central 2015-06-25 /pmc/articles/PMC4479227/ /pubmed/26110022 http://dx.doi.org/10.1186/s13040-015-0052-6 Text en © Waller et al. 2015 This article is published under license to BioMed Central Ltd. 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 work is properly credited. 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 Software Article
Waller, Tomasz
Gubała, Tomasz
Sarapata, Krzysztof
Piwowar, Monika
Jurkowski, Wiktor
DNA microarray integromics analysis platform
title DNA microarray integromics analysis platform
title_full DNA microarray integromics analysis platform
title_fullStr DNA microarray integromics analysis platform
title_full_unstemmed DNA microarray integromics analysis platform
title_short DNA microarray integromics analysis platform
title_sort dna microarray integromics analysis platform
topic Software Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479227/
https://www.ncbi.nlm.nih.gov/pubmed/26110022
http://dx.doi.org/10.1186/s13040-015-0052-6
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