ProteinHistorian

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/.

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

ProteinHistorian is a tool for the identification of protein enrichment by phylogenetic age.

ProteinHistorian

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