Effect of sampling on topology predictions of protein-protein interaction networks

Currently available protein-protein interaction (PPI) network or 'interactome' maps, obtained with the yeast two-hybrid (Y2H) assay or by co-affinity purification followed by mass spectrometry (co-AP/MS), only cover a fraction of the complete PPI networks. These partial networks display sc...

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Bibliographic Details
Published in:Nature biotechnology 2005-07, Vol.23 (7), p.839-844
Main Authors: Bertin, Nicolas, Han, Jing-Dong J, Vidal, Marc, Cusick, Michael E, Dupuy, Denis
Format: Article
Language:English
Subjects:
Agriculture
analysis
Animals
Bioinformatics
Biology
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Cancer
Computational Biology
Computer Simulation
Life Sciences
Mass spectrometry
Network topologies
Protein Interaction Mapping
Proteins
Proteins - chemistry
Proteins - metabolism
Proteomics
Scientific imaging
Topology
Two-Hybrid System Techniques
Yeast
Yeasts
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Description
Summary:Currently available protein-protein interaction (PPI) network or 'interactome' maps, obtained with the yeast two-hybrid (Y2H) assay or by co-affinity purification followed by mass spectrometry (co-AP/MS), only cover a fraction of the complete PPI networks. These partial networks display scale-free topologies–most proteins participate in only a few interactions whereas a few proteins have many interaction partners. Here we analyze whether the scale-free topologies of the partial networks obtained from Y2H assays can be used to accurately infer the topology of complete interactomes. We generated four theoretical interaction networks of different topologies (random, exponential, power law, truncated normal). Partial sampling of these networks resulted in sub-networks with topological characteristics that were virtually indistinguishable from those of currently available Y2H-derived partial interactome maps. We conclude that given the current limited coverage levels, the observed scale-free topology of existing interactome maps cannot be confidently extrapolated to complete interactomes.
ISSN:1087-0156
1546-1696
DOI:10.1038/nbt1116