A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome

@article{Stelzl2005AHP,
  title={A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome},
  author={Ulrich Stelzl and Uwe Worm and Maciej M. Lalowski and Christian Haenig and Felix H. Brembeck and Heike Goehler and Martin Stroedicke and Martina Zenkner and Anke Schoenherr and Susanne Koeppen and Jan Timm and Sascha Mintzlaff and Claudia Abraham and Nicole Bock and S. Kietzmann and Astrid Goedde and Engin Toks{\"o}z and Anja Droege and Sylvia Krobitsch and Bernhard Korn and Walter Birchmeier and Hans Lehrach and Erich E. Wanker},
  journal={Cell},
  year={2005},
  volume={122},
  pages={957-968}
}

Figures and Tables from this paper

Prediction of yeast protein–protein interaction network: insights from the Gene Ontology and annotations

A new method of reconstructing a yeast protein–protein interaction map that is solely based on the GO annotations is proposed, validated using high-quality interaction datasets for its effectiveness and is expected to provide a new approach for predicting the protein– protein interaction maps from other completely sequenced genomes with high- quality GO-based annotations.

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.

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

A computational method is developed that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein- protein interactions in Arabidopsis thaliana, and concludes that the integration of orthology withfunctional association data is adequate to predict protein- proteins interactions.

SPIDer: Saccharomyces protein-protein interaction database

SPIDer is a public database server for protein-protein interactions based on the yeast genome that provides a variety of search options and graphical visualization of an interaction network that will be very useful for the study of inter-member interactions among a list of proteins, especially the protein complex.

Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction

In this chapter, recent efforts to predict interactions between proteins and between protein domains are described and methods that attempt to use protein interaction data to infer protein function are described.

Mining protein-protein interaction networks for the analysis of disease

It is demonstrated that context annotation helps to detect interactions of higher experimental reliability and how context-filtered networks are enriched in bona fide pathways and disease proteins.

Large-scale mapping of human protein–protein interactions by mass spectrometry

In‐depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases, and via the preliminary analysis, many novel protein interactions and pathway associations are reported.

Streamline proteomic approach for characterizing protein-protein interaction network in a RAD52 protein complex.

A strategy of integrating proteomic identification of complex components with mammalian two-hybrid screening of their binary relationships to achieve information content of both breadth and depth in characterizing protein complexes is established.

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.
...

References

SHOWING 1-10 OF 65 REFERENCES

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.

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 network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease.

Functional proteomics mapping of a human signaling pathway.

An integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway is presented, validating this integrated functional proteomics approach.

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

This work quantitatively assesses the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins and introduces the concept of a "regulog"--a conserved regulatory relationship between proteins across different species.

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.

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

These interactions and the accuracy benchmarks will aid interpretation of current functional genomics data and provide a basis for determining the quality of future large-scale human protein interaction assays.

Protein interaction networks from yeast to human.

Functional and topological characterization of protein interaction networks

This work compares four available databases that approximate the protein interaction network of the yeast, Saccharomyces cerevisiae, aiming to uncover the network's generic large‐scale properties and the impact of the proteins' function and cellular localization on the network topology.

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.
...