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Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228777/ https://www.ncbi.nlm.nih.gov/pubmed/22144874 http://dx.doi.org/10.1371/journal.pcbi.1002228 |
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author | Kacmarczyk, Thadeous Waltman, Peter Bate, Ashley Eichenberger, Patrick Bonneau, Richard |
author_facet | Kacmarczyk, Thadeous Waltman, Peter Bate, Ashley Eichenberger, Patrick Bonneau, Richard |
author_sort | Kacmarczyk, Thadeous |
collection | PubMed |
description | The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. |
format | Online Article Text |
id | pubmed-3228777 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32287772011-12-05 Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters Kacmarczyk, Thadeous Waltman, Peter Bate, Ashley Eichenberger, Patrick Bonneau, Richard PLoS Comput Biol Research Article The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. Public Library of Science 2011-12-01 /pmc/articles/PMC3228777/ /pubmed/22144874 http://dx.doi.org/10.1371/journal.pcbi.1002228 Text en Kacmarczyk et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Kacmarczyk, Thadeous Waltman, Peter Bate, Ashley Eichenberger, Patrick Bonneau, Richard Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title_full | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title_fullStr | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title_full_unstemmed | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title_short | Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters |
title_sort | comparative microbial modules resource: generation and visualization of multi-species biclusters |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228777/ https://www.ncbi.nlm.nih.gov/pubmed/22144874 http://dx.doi.org/10.1371/journal.pcbi.1002228 |
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