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A kinetic model of the evolution of a protein interaction network

Overview of attention for article published in BMC Genomics, March 2013
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Title
A kinetic model of the evolution of a protein interaction network
Published in
BMC Genomics, March 2013
DOI 10.1186/1471-2164-14-172
Pubmed ID
Authors

Piotr H Pawlowski, Szymon Kaczanowski, Piotr Zielenkiewicz

Abstract

Known protein interaction networks have very particular properties. Old proteins tend to have more interactions than new ones. One of the best statistical representatives of this property is the node degree distribution (distribution of proteins having a given number of interactions). It has previously been shown that this distribution is very close to the sum of two distinct exponential components. In this paper, we asked: What are the possible mechanisms of evolution for such types of networks? To answer this question, we tested a kinetic model for simplified evolution of a protein interactome. Our proposed model considers the emergence of new genes and interactions and the loss of old ones. We assumed that there are generally two coexisting classes of proteins. Proteins constituting the first class are essential only for ecological adaptations and are easily lost when ecological conditions change. Proteins of the second class are essential for basic life processes and, hence, are always effectively protected against deletion. All proteins can transit between the above classes in both directions. We also assumed that the phenomenon of gene duplication is always related to ecological adaptation and that a new copy of a duplicated gene is not essential. According to this model, all proteins gain new interactions with a rate that preferentially increases with the number of interactions (the rich get richer). Proteins can also gain interactions because of duplication. Proteins lose their interactions both with and without the loss of partner genes.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 4%
Netherlands 1 4%
Unknown 26 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 46%
Researcher 3 11%
Student > Postgraduate 3 11%
Professor 2 7%
Professor > Associate Professor 2 7%
Other 1 4%
Unknown 4 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 46%
Biochemistry, Genetics and Molecular Biology 6 21%
Computer Science 2 7%
Mathematics 2 7%
Unknown 5 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 19 March 2013.
All research outputs
#15,169,949
of 25,374,917 outputs
Outputs from BMC Genomics
#5,391
of 11,244 outputs
Outputs of similar age
#116,858
of 209,244 outputs
Outputs of similar age from BMC Genomics
#86
of 186 outputs
Altmetric has tracked 25,374,917 research outputs across all sources so far. This one is in the 38th percentile – i.e., 38% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,244 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 49th percentile – i.e., 49% of its peers scored the same or lower than it.
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 209,244 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 186 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.