GenoSets: visual analytic methods for comparative genomics.

Many important questions in biology are, fundamentally, comparative, and this extends to our analysis of a growing number of sequenced genomes. Existing genomic analysis tools are often organized around literal views of genomes as linear strings. Even when information is highly condensed, these view...

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Autores principales:	Aurora A Cain, Robert Kosara, Cynthia J Gibas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5b24bb30ee004026be0d920b97197b42
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spelling	oai:doaj.org-article:5b24bb30ee004026be0d920b97197b422021-11-18T08:13:22ZGenoSets: visual analytic methods for comparative genomics.1932-620310.1371/journal.pone.0046401https://doaj.org/article/5b24bb30ee004026be0d920b97197b422012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23056299/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Many important questions in biology are, fundamentally, comparative, and this extends to our analysis of a growing number of sequenced genomes. Existing genomic analysis tools are often organized around literal views of genomes as linear strings. Even when information is highly condensed, these views grow cumbersome as larger numbers of genomes are added. Data aggregation and summarization methods from the field of visual analytics can provide abstracted comparative views, suitable for sifting large multi-genome datasets to identify critical similarities and differences. We introduce a software system for visual analysis of comparative genomics data. The system automates the process of data integration, and provides the analysis platform to identify and explore features of interest within these large datasets. GenoSets borrows techniques from business intelligence and visual analytics to provide a rich interface of interactive visualizations supported by a multi-dimensional data warehouse. In GenoSets, visual analytic approaches are used to enable querying based on orthology, functional assignment, and taxonomic or user-defined groupings of genomes. GenoSets links this information together with coordinated, interactive visualizations for both detailed and high-level categorical analysis of summarized data. GenoSets has been designed to simplify the exploration of multiple genome datasets and to facilitate reasoning about genomic comparisons. Case examples are included showing the use of this system in the analysis of 12 Brucella genomes. GenoSets software and the case study dataset are freely available at http://genosets.uncc.edu. We demonstrate that the integration of genomic data using a coordinated multiple view approach can simplify the exploration of large comparative genomic data sets, and facilitate reasoning about comparisons and features of interest.Aurora A CainRobert KosaraCynthia J GibasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e46401 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aurora A Cain Robert Kosara Cynthia J Gibas GenoSets: visual analytic methods for comparative genomics.
description	Many important questions in biology are, fundamentally, comparative, and this extends to our analysis of a growing number of sequenced genomes. Existing genomic analysis tools are often organized around literal views of genomes as linear strings. Even when information is highly condensed, these views grow cumbersome as larger numbers of genomes are added. Data aggregation and summarization methods from the field of visual analytics can provide abstracted comparative views, suitable for sifting large multi-genome datasets to identify critical similarities and differences. We introduce a software system for visual analysis of comparative genomics data. The system automates the process of data integration, and provides the analysis platform to identify and explore features of interest within these large datasets. GenoSets borrows techniques from business intelligence and visual analytics to provide a rich interface of interactive visualizations supported by a multi-dimensional data warehouse. In GenoSets, visual analytic approaches are used to enable querying based on orthology, functional assignment, and taxonomic or user-defined groupings of genomes. GenoSets links this information together with coordinated, interactive visualizations for both detailed and high-level categorical analysis of summarized data. GenoSets has been designed to simplify the exploration of multiple genome datasets and to facilitate reasoning about genomic comparisons. Case examples are included showing the use of this system in the analysis of 12 Brucella genomes. GenoSets software and the case study dataset are freely available at http://genosets.uncc.edu. We demonstrate that the integration of genomic data using a coordinated multiple view approach can simplify the exploration of large comparative genomic data sets, and facilitate reasoning about comparisons and features of interest.
format	article
author	Aurora A Cain Robert Kosara Cynthia J Gibas
author_facet	Aurora A Cain Robert Kosara Cynthia J Gibas
author_sort	Aurora A Cain
title	GenoSets: visual analytic methods for comparative genomics.
title_short	GenoSets: visual analytic methods for comparative genomics.
title_full	GenoSets: visual analytic methods for comparative genomics.
title_fullStr	GenoSets: visual analytic methods for comparative genomics.
title_full_unstemmed	GenoSets: visual analytic methods for comparative genomics.
title_sort	genosets: visual analytic methods for comparative genomics.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/5b24bb30ee004026be0d920b97197b42
work_keys_str_mv	AT auroraacain genosetsvisualanalyticmethodsforcomparativegenomics AT robertkosara genosetsvisualanalyticmethodsforcomparativegenomics AT cynthiajgibas genosetsvisualanalyticmethodsforcomparativegenomics
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GenoSets: visual analytic methods for comparative genomics.

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