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

  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 A. Doucette-Stamm and Michael E. Cusick and David E. Hill and Frederick P. Roth and Marc Vidal},
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… 

Network biology: A protein network of one's own proteins

  • M. Skipper
  • Biology
    Nature Reviews Molecular Cell Biology
  • 2005
Two recent reports provide the first 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.

Comparison of Human Protein-Protein Interaction Maps

A first comparative analysis of eight currently available large-scale maps of protein-protein interactions based on literature search, orthology or by yeast-two-hybrid assays gives clear indications that all interaction maps imply considerable selection and detection biases.

Interactome: gateway into systems biology.

Although far from complete, currently available maps provide insight into how biochemical properties of proteins and protein complexes are integrated into biological systems, and are also a useful resource to predict the function(s) of thousands of genes.

Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

This work introduces a novel method, maximum specificity set cover (MSSC), for the prediction of protein-protein interactions, and shows that MSSC reliably predicts protein interactions in well-studied molecular systems, such as the 26S proteasome and RNA polymerase II of S. cerevisiae.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

This meta‐analysis exploits non‐protein‐based data, but successfully predicts associations, including 5589 novel human physical protein associations, with measured accuracies of 54±10%, comparable to direct large‐scale interaction assays.

A reference map of the human binary protein interactome

The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.

A computational interactome and functional annotation for the human proteome

It is shown, using Gene Set Enrichment Analysis (GSEA), that predicted interaction partners can be used to annotate a protein’s function and most human proteins, including many annotated as having unknown function, are provided.

High-quality binary interactome mapping.

Architecture of the human interactome defines protein communities and disease networks

With more than 56,000 candidate interactions, BioPlex 2.0 exceeds previous experimentally derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biology of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

Through affinity-purification mass spectrometry, two proteome-scale, cell-line-specific interaction networks are created that define principles of proteome organization and enable unknown protein characterization.



A first-draft human protein-interaction map

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.

Functional organization of the yeast proteome by systematic analysis of protein complexes

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.

A comprehensive two-hybrid analysis to explore the yeast protein interactome

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.

A Protein Interaction Map of Drosophila melanogaster

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.

A Map of the Interactome Network of the Metazoan C. elegans

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.

Evidence for dynamically organized modularity in the yeast protein–protein interaction network

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.

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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.

Protein interaction mapping: a Drosophila case study.

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.

Development of human protein reference database as an initial platform for approaching systems biology in humans.

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.

The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes.

  • A. Wagner
  • Biology
    Molecular biology and evolution
  • 2001
The structure and evolution of the protein interaction network of the yeast Saccharomyces cerevisiae is analyzed and it is shown that the persistence of redundant interaction partners is the exception rather than the rule.