Document Detail


Dense graphlet statistics of protein interaction and random networks.
MedLine Citation:
PMID:  19213135     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Understanding evolutionary dynamics from a systemic point of view crucially depends on knowledge about how evolution affects size and structure of the organisms' functional building blocks (modules). It has been recently reported that statistics over sparse PPI graphlets can robustly monitor such evolutionary changes. However, there is abundant evidence that in PPI networks modules can be identified with highly interconnected (dense) and/or bipartite subgraphs. We count such dense graphlets in PPI networks by employing recently developed search strategies that render related inference problems tractable. We demonstrate that corresponding counting statistics differ significantly between prokaryotes and eukaryotes as well as between "real" PPI networks and scale free network emulators. We also prove that another class of emulators, the low-dimensional geometric random graphs (GRGs) cannot contain a specific type of motifs, complete bipartite graphs, which are abundant in PPI networks.
Authors:
R Colak; F Hormozdiari; F Moser; A Schönhuth; J Holman; M Ester; S C Sahinalp
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing     Volume:  -     ISSN:  2335-6936     ISO Abbreviation:  Pac Symp Biocomput     Publication Date:  2009  
Date Detail:
Created Date:  2009-02-12     Completed Date:  2009-03-12     Revised Date:  2013-02-20    
Medline Journal Info:
Nlm Unique ID:  9711271     Medline TA:  Pac Symp Biocomput     Country:  Singapore    
Other Details:
Languages:  eng     Pagination:  178-89     Citation Subset:  IM    
Affiliation:
School of Computing Science, Simon Fraser University.
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MeSH Terms
Descriptor/Qualifier:
Biometry
Escherichia coli Proteins / chemistry,  genetics
Evolution, Molecular
Models, Biological
Protein Interaction Domains and Motifs
Protein Interaction Mapping / statistics & numerical data*
Saccharomyces cerevisiae Proteins / chemistry,  genetics
Chemical
Reg. No./Substance:
0/Escherichia coli Proteins; 0/Saccharomyces cerevisiae Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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