Design principles of molecular networks revealed by global comparisons and composite motifs.

Design principles of molecular networks revealed by global comparisons and composite motifs. Research Abstract Details 

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Design principles of molecular networks revealed by global comparisons and composite motifs. Abstract Text:

Haiyuan Yu,Yu Xia,Valery Trifonov,Mark Gerstein,

BACKGROUND: Molecular networks are of current interest, particularly with the publication of many large-scale datasets. Previous analyses have focused on topologic structures of individual networks. RESULTS: Here, we present a global comparison of four basic molecular networks: regulatory, co-expression, interaction, and metabolic. In terms of overall topologic correlation--whether nearby proteins in one network are close in another--we find that the four are quite similar. However, focusing on the occurrence of local features, we introduce the concept of composite hubs, namely hubs shared by more than one network. We find that the three 'action' networks (metabolic, co-expression, and interaction) share the same scaffolding of hubs, whereas the regulatory network uses distinctly different regulator hubs. Finally, we examine the inter-relationship between the regulatory network and the three action networks, focusing on three composite motifs--triangles, trusses, and bridges--involving different degrees of regulation of gene pairs. Our analysis shows that interaction and co-expression networks have short-range relationships, with directly interacting and co-expressed proteins sharing regulators. However, the metabolic network contains many long-distance relationships: far-away enzymes in a pathway often have time-delayed expression relationships, which are well coordinated by bridges connecting their regulators. CONCLUSION: We demonstrate how basic molecular networks are distinct yet connected and well coordinated. Many of our conclusions can be mapped onto structured social networks, providing intuitive comparisons. In particular, the long-distance regulation in metabolic networks agrees with its counterpart in social networks (namely, assembly lines). Conversely, the segregation of regulator hubs from other hubs diverges from social intuitions (as managers often are centers of interactions).

Design principles of molecular networks revealed by global comparisons and composite motifs. Publishing Authors By Initials

H Yu,Y Xia,V Trifonov,M Gerstein,

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Design principles of molecular networks revealed by global comparisons and composite motifs. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Genome biology

VOLUME: 7

Page Numbers: R55

Journal Abbreviation: Genome Biol.

ISSN: 1465-6914

DAY: 3

MONTH: 12

YEAR: 2006

Design principles of molecular networks revealed by global comparisons and composite motifs. Information

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LANGUAGE: eng

NlmUniqueID: 100960660

Design principles of molecular networks revealed by global comparisons and composite motifs. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: Design principles of molecular networks revealed by global comparisons and composite motifs. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Design principles of molecular networks revealed by global comparisons and composite motifs.

AFFILIATION: Department of Molecular Biophysics and Biochemistry, Whitney Avenue, Yale University, New Haven, CT 06520, USA.

Country: England

AGENCY: United States NIGMS

GRANT: P50 GM62413-01

ACRONYM: GM

MEDLINETA: Genome Biol

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