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The Omics Dashboard for interactive exploration of gene-expression data

The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, ener...

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Autores principales: Paley, Suzanne, Parker, Karen, Spaulding, Aaron, Tomb, Jean-Francois, O’Maille, Paul, Karp, Peter D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716103/
https://www.ncbi.nlm.nih.gov/pubmed/29040755
http://dx.doi.org/10.1093/nar/gkx910
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author Paley, Suzanne
Parker, Karen
Spaulding, Aaron
Tomb, Jean-Francois
O’Maille, Paul
Karp, Peter D.
author_facet Paley, Suzanne
Parker, Karen
Spaulding, Aaron
Tomb, Jean-Francois
O’Maille, Paul
Karp, Peter D.
author_sort Paley, Suzanne
collection PubMed
description The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, energy metabolism, regulation and central dogma. Each of those panels contains a series of X–Y plots depicting expression levels of subsystems of that panel, e.g. subsystems within the central dogma panel include transcription, translation and protein maturation and folding. The Dashboard presents a visual read-out of the expression status of cellular systems to facilitate a rapid top-down user survey of how all cellular systems are responding to a given stimulus, and to enable the user to quickly view the responses of genes within specific systems of interest. Although the Dashboard is complementary to traditional statistical methods for analysis of gene-expression data, we show how it can detect changes in gene expression that statistical techniques may overlook. We present the capabilities of the Dashboard using two case studies: the analysis of lipid production for the marine alga Thalassiosira pseudonana, and an investigation of a shift from anaerobic to aerobic growth for the bacterium Escherichia coli.
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spelling pubmed-57161032017-12-08 The Omics Dashboard for interactive exploration of gene-expression data Paley, Suzanne Parker, Karen Spaulding, Aaron Tomb, Jean-Francois O’Maille, Paul Karp, Peter D. Nucleic Acids Res Computational Biology The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, energy metabolism, regulation and central dogma. Each of those panels contains a series of X–Y plots depicting expression levels of subsystems of that panel, e.g. subsystems within the central dogma panel include transcription, translation and protein maturation and folding. The Dashboard presents a visual read-out of the expression status of cellular systems to facilitate a rapid top-down user survey of how all cellular systems are responding to a given stimulus, and to enable the user to quickly view the responses of genes within specific systems of interest. Although the Dashboard is complementary to traditional statistical methods for analysis of gene-expression data, we show how it can detect changes in gene expression that statistical techniques may overlook. We present the capabilities of the Dashboard using two case studies: the analysis of lipid production for the marine alga Thalassiosira pseudonana, and an investigation of a shift from anaerobic to aerobic growth for the bacterium Escherichia coli. Oxford University Press 2017-12-01 2017-10-13 /pmc/articles/PMC5716103/ /pubmed/29040755 http://dx.doi.org/10.1093/nar/gkx910 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Computational Biology
Paley, Suzanne
Parker, Karen
Spaulding, Aaron
Tomb, Jean-Francois
O’Maille, Paul
Karp, Peter D.
The Omics Dashboard for interactive exploration of gene-expression data
title The Omics Dashboard for interactive exploration of gene-expression data
title_full The Omics Dashboard for interactive exploration of gene-expression data
title_fullStr The Omics Dashboard for interactive exploration of gene-expression data
title_full_unstemmed The Omics Dashboard for interactive exploration of gene-expression data
title_short The Omics Dashboard for interactive exploration of gene-expression data
title_sort omics dashboard for interactive exploration of gene-expression data
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716103/
https://www.ncbi.nlm.nih.gov/pubmed/29040755
http://dx.doi.org/10.1093/nar/gkx910
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