ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight int...

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Autores principales:	John A Capra, Alexander G Williams, Katherine S Pollard
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0ff7128c7a1d490eb8973184fbad7e47
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spelling	oai:doaj.org-article:0ff7128c7a1d490eb8973184fbad7e472021-11-18T05:51:13ZProteinHistorian: tools for the comparative analysis of eukaryote protein origin.1553-734X1553-735810.1371/journal.pcbi.1002567https://doaj.org/article/0ff7128c7a1d490eb8973184fbad7e472012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22761559/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/.John A CapraAlexander G WilliamsKatherine S PollardPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 6, p e1002567 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 John A Capra Alexander G Williams Katherine S Pollard ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
description	The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/.
format	article
author	John A Capra Alexander G Williams Katherine S Pollard
author_facet	John A Capra Alexander G Williams Katherine S Pollard
author_sort	John A Capra
title	ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
title_short	ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
title_full	ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
title_fullStr	ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
title_full_unstemmed	ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
title_sort	proteinhistorian: tools for the comparative analysis of eukaryote protein origin.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0ff7128c7a1d490eb8973184fbad7e47
work_keys_str_mv	AT johnacapra proteinhistoriantoolsforthecomparativeanalysisofeukaryoteproteinorigin AT alexandergwilliams proteinhistoriantoolsforthecomparativeanalysisofeukaryoteproteinorigin AT katherinespollard proteinhistoriantoolsforthecomparativeanalysisofeukaryoteproteinorigin
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ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

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