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PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications

Overview of attention for article published in BMC Genomics, August 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)
  • High Attention Score compared to outputs of the same age and source (81st percentile)

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8 X users
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1 patent

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21 Dimensions

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70 Mendeley
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Title
PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
Published in
BMC Genomics, August 2015
DOI 10.1186/s12864-015-1820-x
Pubmed ID
Authors

Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James, Jean Yee Hwa Yang

Abstract

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus. PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 70 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 1%
Brazil 1 1%
Unknown 68 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 29%
Researcher 14 20%
Student > Master 9 13%
Professor > Associate Professor 5 7%
Student > Bachelor 3 4%
Other 9 13%
Unknown 10 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 21 30%
Biochemistry, Genetics and Molecular Biology 11 16%
Computer Science 4 6%
Engineering 3 4%
Chemistry 3 4%
Other 11 16%
Unknown 17 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 7. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 March 2022.
All research outputs
#5,159,720
of 25,205,864 outputs
Outputs from BMC Genomics
#1,995
of 11,189 outputs
Outputs of similar age
#59,977
of 272,213 outputs
Outputs of similar age from BMC Genomics
#46
of 252 outputs
Altmetric has tracked 25,205,864 research outputs across all sources so far. Compared to these this one has done well and is in the 79th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 11,189 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done well, scoring higher than 82% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 272,213 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 78% of its contemporaries.
We're also able to compare this research output to 252 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 81% of its contemporaries.