Towards a proteome-scale map of the human protein–protein interaction network

@article{Rual2005TowardsAP,
  title={Towards a proteome-scale map of the human protein–protein interaction network},
  author={Jean-François Rual and Kavitha Venkatesan and Tong Hao and Tomoko Hirozane-Kishikawa and Am{\'e}lie Dricot and Ning Li and Gabriel F. Berriz and Francis D. Gibbons and Matija Dreze and Nono Ayivi-Guedehoussou and Niels Klitgord and Christophe Simon and Mike Boxem and Stuart Milstein and Jennifer Rosenberg and Debra Goldberg and Lan V. Zhang and Sharyl L. Wong and G. Franklin and Siming Li and Joanna S. Albala and Janghoo Lim and Carlene Fraughton and Estelle Llamosas and Sebiha Cevik and Camille Choma Bex and Philippe Lamesch and Robert S. Sikorski and Jean Vandenhaute and Huda Y. Zoghbi and Alex Smolyar and Stephanie A Bosak and Reynaldo Sequerra and Lynn Doucette‐Stamm and Michael E. Cusick and David E. Hill and Frederick P. Roth and Marc Vidal},
  journal={Nature},
  year={2005},
  volume={437},
  pages={1173-1178}
}
Systematic mapping of protein–protein interactions, or ‘interactome’ mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we… Expand
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Two recent reports provide the first experimentally derived description of a human protein–protein interaction network, which seems to have scale-free properties and to evolve by preferentially adding interactions between lineage-specific proteins. Expand
Network biology: A protein network of one's own proteins
  • M. Skipper
  • Biology
  • Nature Reviews Molecular Cell Biology
  • 2005
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References

SHOWING 1-10 OF 39 REFERENCES
A first-draft human protein-interaction map
TLDR
A network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps is described, and it is shown how the network can be used to successfully predict the functions of human proteins. Expand
Functional organization of the yeast proteome by systematic analysis of protein complexes
TLDR
The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery. Expand
A comprehensive two-hybrid analysis to explore the yeast protein interactome
TLDR
The comprehensive analysis using a system to examine two-hybrid interactions in all possible combinations between the budding yeast Saccharomyces cerevisiae is completed and would significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system. Expand
A Protein Interaction Map of Drosophila melanogaster
TLDR
This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans, and recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. Expand
A Map of the Interactome Network of the Metazoan C. elegans
TLDR
A large fraction of the Caenorhabditis elegans interactome network is mapped, starting with a subset of metazoan-specific proteins, and more than 4000 interactions were identified from high-throughput, yeast two-hybrid screens. Expand
Evidence for dynamically organized modularity in the yeast protein–protein interaction network
TLDR
This work investigated how hubs might contribute to robustness and other cellular properties for protein–protein interactions dynamically regulated both in time and in space, and uncovered two types of hub: ‘party’ hubs, which interact with most of their partners simultaneously, and ‘date’ Hubs, which bind their different partners at different times or locations. Expand
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
TLDR
Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. Expand
Protein interaction mapping: a Drosophila case study.
TLDR
This work used a high-throughput yeast two-hybrid (Y2H)-based technology to screen 102 bait proteins from Drosophila melanogaster, most of them orthologous to human cancer-related and/or signaling proteins, against high-complexity fly cDNA libraries. Expand
An automated method for finding molecular complexes in large protein interaction networks
TLDR
A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described. Expand
Development of human protein reference database as an initial platform for approaching systems biology in humans.
TLDR
This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era. Expand
...
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