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Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree
Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740139/ https://www.ncbi.nlm.nih.gov/pubmed/23940838 http://dx.doi.org/10.7717/peerj.126 |
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author | Chartier, Matthieu Chénard, Thierry Barker, Jonathan Najmanovich, Rafael |
author_facet | Chartier, Matthieu Chénard, Thierry Barker, Jonathan Najmanovich, Rafael |
author_sort | Chartier, Matthieu |
collection | PubMed |
description | Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains 518 members. Most studies that focus on the human kinome require, at some point, the visualization of large amounts of data. The visualization of such data within the framework of a phylogenetic tree may help identify key relationships between different protein kinases in view of their evolutionary distance and the information used to annotate the kinome tree. For example, studies that focus on the promiscuity of kinase inhibitors can benefit from the annotations to depict binding affinities across kinase groups. Images involving the mapping of information into the kinome tree are common. However, producing such figures manually can be a long arduous process prone to errors. To circumvent this issue, we have developed a web-based tool called Kinome Render (KR) that produces customized annotations on the human kinome tree. KR allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on the human kinome tree. The web interface can be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A stand-alone version is also available and can be run locally. |
format | Online Article Text |
id | pubmed-3740139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-37401392013-08-12 Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree Chartier, Matthieu Chénard, Thierry Barker, Jonathan Najmanovich, Rafael PeerJ Bioinformatics Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains 518 members. Most studies that focus on the human kinome require, at some point, the visualization of large amounts of data. The visualization of such data within the framework of a phylogenetic tree may help identify key relationships between different protein kinases in view of their evolutionary distance and the information used to annotate the kinome tree. For example, studies that focus on the promiscuity of kinase inhibitors can benefit from the annotations to depict binding affinities across kinase groups. Images involving the mapping of information into the kinome tree are common. However, producing such figures manually can be a long arduous process prone to errors. To circumvent this issue, we have developed a web-based tool called Kinome Render (KR) that produces customized annotations on the human kinome tree. KR allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on the human kinome tree. The web interface can be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A stand-alone version is also available and can be run locally. PeerJ Inc. 2013-08-08 /pmc/articles/PMC3740139/ /pubmed/23940838 http://dx.doi.org/10.7717/peerj.126 Text en © 2013 Chartier et al. http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Bioinformatics Chartier, Matthieu Chénard, Thierry Barker, Jonathan Najmanovich, Rafael Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title | Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title_full | Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title_fullStr | Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title_full_unstemmed | Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title_short | Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
title_sort | kinome render: a stand-alone and web-accessible tool to annotate the human protein kinome tree |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740139/ https://www.ncbi.nlm.nih.gov/pubmed/23940838 http://dx.doi.org/10.7717/peerj.126 |
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