NDLI: The identification of functional modules from the genomic association of genes.

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The identification of functional modules from the genomic association of genes.

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The identification of functional modules from the genomic association of genes.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Bork, Peer Snel, Berend Huynen, Martijn A.
Description	Author Affiliation: Snel B ( European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. snel@embl-heidelberg.de);
Abstract	By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of such networks to identify functional modules: sets of proteins that together are involved in a biological process. The complete network contains 3,033 orthologous groups of proteins in 38 genomes. It consists of one giant component, containing 1,611 orthologous groups, and of 516 small disjointed clusters that, on average, contain only 2.7 orthologous groups. These small clusters have a homogeneous functional composition and thus represent functional modules in themselves. Analysis of the giant component reveals that it is a scale-free, small-world network with a high degree of local clustering (C = 0.6). It consists of locally highly connected subclusters that are connected to each other by linker proteins. The linker proteins tend to have multiple functions, or are involved in multiple processes and have an above average probability of being essential. By splitting up the giant component at these linker proteins, we identify 265 subclusters that tend to have a homogeneous functional composition. The rare functional inhomogeneities in our subclusters reflect the mixing of different types of (molecular) functions in a single cellular process, exemplified by subclusters containing both metabolic enzymes as well as the transcription factors that regulate them. Comparative genome analysis, thus, allows identification of a level of functional interaction between that of pairwise interactions, and of the complete genome.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	9
Volume Number	99
Language	English
Publisher	National Academy of Sciences
Publisher Date	2002-05-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Genome Models, Genetic Animals Databases As Topic Multigene Family Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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