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Co-expression of cell-wall related genes: new tools and insights
Global transcript analyses based on publicly available microarray dataset have revealed that genes with similar function tend to be transcriptionally coordinated. Indeed, many genes involved in the formation of cellulose, hemicelluloses, and lignin have been identified using co-expression approaches...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Research Foundation
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355730/ https://www.ncbi.nlm.nih.gov/pubmed/22645599 http://dx.doi.org/10.3389/fpls.2012.00083 |
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author | Ruprecht, Colin Persson, Staffan |
author_facet | Ruprecht, Colin Persson, Staffan |
author_sort | Ruprecht, Colin |
collection | PubMed |
description | Global transcript analyses based on publicly available microarray dataset have revealed that genes with similar function tend to be transcriptionally coordinated. Indeed, many genes involved in the formation of cellulose, hemicelluloses, and lignin have been identified using co-expression approaches in Arabidopsis. To facilitate these transcript analyses, several web-based tools have been developed that allow researchers to investigate co-expression relationships of their gene(s) of interest. In addition, several tools now also provide the possibility of comparative transcriptional analyses across species, which potentially increases the predictive power. In this short review, we describe recent developments and updates of plant-related co-expression tools, and summarize studies that have successfully used expression profiling in cell wall research. Finally, we illustrate the value of comparative co-expression relationships across species using genes involved in lignin biosynthesis. |
format | Online Article Text |
id | pubmed-3355730 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Frontiers Research Foundation |
record_format | MEDLINE/PubMed |
spelling | pubmed-33557302012-05-29 Co-expression of cell-wall related genes: new tools and insights Ruprecht, Colin Persson, Staffan Front Plant Sci Plant Science Global transcript analyses based on publicly available microarray dataset have revealed that genes with similar function tend to be transcriptionally coordinated. Indeed, many genes involved in the formation of cellulose, hemicelluloses, and lignin have been identified using co-expression approaches in Arabidopsis. To facilitate these transcript analyses, several web-based tools have been developed that allow researchers to investigate co-expression relationships of their gene(s) of interest. In addition, several tools now also provide the possibility of comparative transcriptional analyses across species, which potentially increases the predictive power. In this short review, we describe recent developments and updates of plant-related co-expression tools, and summarize studies that have successfully used expression profiling in cell wall research. Finally, we illustrate the value of comparative co-expression relationships across species using genes involved in lignin biosynthesis. Frontiers Research Foundation 2012-05-03 /pmc/articles/PMC3355730/ /pubmed/22645599 http://dx.doi.org/10.3389/fpls.2012.00083 Text en Copyright © Ruprecht and Persson. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) , which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited. |
spellingShingle | Plant Science Ruprecht, Colin Persson, Staffan Co-expression of cell-wall related genes: new tools and insights |
title | Co-expression of cell-wall related genes: new tools and insights |
title_full | Co-expression of cell-wall related genes: new tools and insights |
title_fullStr | Co-expression of cell-wall related genes: new tools and insights |
title_full_unstemmed | Co-expression of cell-wall related genes: new tools and insights |
title_short | Co-expression of cell-wall related genes: new tools and insights |
title_sort | co-expression of cell-wall related genes: new tools and insights |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355730/ https://www.ncbi.nlm.nih.gov/pubmed/22645599 http://dx.doi.org/10.3389/fpls.2012.00083 |
work_keys_str_mv | AT ruprechtcolin coexpressionofcellwallrelatedgenesnewtoolsandinsights AT perssonstaffan coexpressionofcellwallrelatedgenesnewtoolsandinsights |