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.
journal_name
Proc Natl Acad Sci U S Aauthors
Snel B,Bork P,Huynen MAdoi
10.1073/pnas.092632599keywords:
subject
Has Abstractpub_date
2002-04-30 00:00:00pages
5890-5issue
9eissn
0027-8424issn
1091-6490pii
99/9/5890journal_volume
99pub_type
杂志文章abstract::Phosphoenolpyruvate carboxykinase (GTP) [GTP;oxaloacetate carboxy-lyase(transphosphorylating); EC 4.1.1.32] is absent in rat liver cytosol during fetal life and is synthesized initially at birth. De novo synthesis of the enzyme can be induced prematurely by injection of dibutyryl cyclic AMP or glucagon into fetal anim...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
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更新日期:2004-03-30 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1990-09-01 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
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更新日期:2009-04-21 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1986-06-01 00:00:00