Graph theoretic analysis of protein interaction networks of eukaryotes

Kwang-Il Goh, B. Kahng, D. Kim

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Owing to the recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high-throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are conserved across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interologs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interolog additions, for which we present a possible scenario through an in silico modeling.

Original languageEnglish
Pages (from-to)501-512
Number of pages12
JournalPhysica A: Statistical Mechanics and its Applications
Volume357
Issue number3-4
DOIs
Publication statusPublished - 2005 Nov 15
Externally publishedYes

Fingerprint

eukaryotes
Protein Interaction Networks
Yeast
Structural Properties
yeast
Worm
Modularity
proteins
modularity
worms
High Throughput
Connectivity
Graph in graph theory
Generic Property
Drosophilidae
interactions
Fruit
Hybrid Method
Drosophila
False Positive

Keywords

  • Degree correlation
  • Modularity
  • Protein interaction network

ASJC Scopus subject areas

  • Mathematical Physics
  • Statistical and Nonlinear Physics

Cite this

Graph theoretic analysis of protein interaction networks of eukaryotes. / Goh, Kwang-Il; Kahng, B.; Kim, D.

In: Physica A: Statistical Mechanics and its Applications, Vol. 357, No. 3-4, 15.11.2005, p. 501-512.

Research output: Contribution to journalArticle

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