Protein-interaction networks: from experiments to analysis.

Functional proteomics approaches aim to characterize comprehensively the function of gene products, and provide a first-level understanding of cellular mechanisms. Here, we review recent techniques for the construction and prediction of large-scale protein-interaction networks, with a particular emphasis on computational processing steps and comparative assessment of the reliability and completeness of the various approaches. We also discuss the use of protein-interaction network information in functional annotation and in the generation of higher-level biological hypotheses on pathways.

[1]  Ian Dix,et al.  Yeast Yeast 2000; 17: 95±110. Research Article , 2000 .

[2]  S. Fields,et al.  Genome-wide analysis of vaccinia virus protein-protein interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[3]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[4]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[5]  P. Legrain,et al.  Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens , 1997, Nature Genetics.

[6]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[7]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 2000, Nucleic Acids Res..

[8]  S. Fields,et al.  Protein-protein interactions: methods for detection and analysis , 1995, Microbiological reviews.

[9]  J M Gauthier,et al.  Protein--protein interaction maps: a lead towards cellular functions. , 2001, Trends in genetics : TIG.

[10]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[11]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[12]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[13]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.

[14]  B. Schwikowski,et al.  A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.

[15]  T. Jenssen,et al.  A literature network of human genes for high-throughput analysis of gene expression , 2001 .

[16]  M. Vidal,et al.  Protein interaction maps for model organisms , 2001, Nature Reviews Molecular Cell Biology.

[17]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[18]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[19]  M. Vidal,et al.  Yeast forward and reverse 'n'-hybrid systems. , 1999, Nucleic acids research.

[20]  V. Schächter Construction and prediction of protein-protein interaction maps. , 2002, Ernst Schering Research Foundation workshop.

[21]  Norman W. Paton,et al.  INTERACT: An Object Oriented Protein-Protein Interaction Database , 1999, ISMB.

[22]  T. Ito,et al.  Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[25]  D. Eisenberg,et al.  Protein function in the post-genomic era , 2000, Nature.

[26]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Miguel A. Andrade-Navarro,et al.  Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions , 1999, ISMB.

[28]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Toshihisa Takagi,et al.  Automated extraction of information on protein-protein interactions from the biological literature , 2001, Bioinform..

[30]  Michael E. Cusick,et al.  The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information , 2000, Nucleic Acids Res..

[31]  Stanley Fields,et al.  A protein linkage map of Escherichia coli bacteriophage T7 , 1996, Nature Genetics.

[32]  G. Dreyfuss,et al.  Functional Conservation of the Transportin Nuclear Import Pathway in Divergent Organisms , 1998, Molecular and Cellular Biology.

[33]  Jérôme Euzenat,et al.  Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database , 1999, Nucleic Acids Res..

[34]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[35]  E. Wolf,et al.  A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  P. Legrain,et al.  A genomic approach of the hepatitis C virus generates a protein interaction map. , 2000, Gene.

[38]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[39]  Melanie L. Mayer,et al.  Protein networks—built by association , 2000, Nature Biotechnology.