A computational interactome and functional annotation for the human proteome
- Columbia University, United States
Abstract
We present a database, PrePPI (Predicting Protein-Protein Interactions), of more than 1.35 million predicted protein-protein interactions (PPIs). Of these at least 127,000 are expected to constitute direct physical interactions although the actual number may be much larger (~500,000). The current PrePPI, which contains predicted interactions for about 85% of the human proteome is related to an earlier version but is based on additional sources of interaction evidence and is far larger in scope. The use of structural relationships allows PrePPI to infer numerous previously unreported interactions. PrePPI has been subjected to a series of validation tests including reproducing known interactions, recapitulating multi-protein complexes, analysis of disease associated SNPs, and identifying functional relationships between interacting proteins. We show, using Gene Set Enrichment Analysis (GSEA), that predicted interaction partners can be used to annotate a protein's function. We provide annotations for most human proteins, including many annotated as having unknown function.
Data availability
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Coexpression data for C. elegansPublicly available at Coexpressdb (accession no: Cel.c2-0).
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Coexpression data for dogPublicly available at Coexpressdb (accession no: Cfa.c1-0).
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Coexpression data for fruit flyPublicly available at Coexpressdb (accession no: Dme.c2-0).
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Coexpression data for zebrafishPublicly available at Coexpressdb (accession no: Dre.c2-0).
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Coexpression data for chickenPublicly available at Coexpressdb (accession no: Gga.c2-0).
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Coexpression data for humanPublicly available at Coexpressdb (accession no: Hsa.c4-0).
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Coexpression data for humanPublicly available at Coexpressdb (accession no: Hsa2.c1-0).
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Coexpression data for rhesus monkeyPublicly available at Coexpressdb (accession no: Mcc.c1-0).
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Coexpression data for mousePublicly available at Coexpressdb (accession no: Mmu.c3-0).
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Coexpression data for Norway ratPublicly available at Coexpressdb (accession no: Rno.c2-0).
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Coexpression data for budding yeastPublicly available at Coexpressdb (accession no: Sce.c1-0).
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Coexpression data for fission yeastPublicly available at Coexpressdb (accession no: Spo.c1-0).
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Coexpression data for humanPublicly available at Array Express.
Article and author information
Author details
Funding
National Institutes of Health (GM030518)
- Barry Honig
National Institutes of Health (S10OD012351)
- José Ignacio Garzón
- Lei Deng
- Diana Murray
- Sagi Shapira
- Donald Petrey
- Barry Honig
National Institutes of Health (S10OD021764)
- José Ignacio Garzón
- Lei Deng
- Diana Murray
- Sagi Shapira
- Donald Petrey
- Barry Honig
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2016, Garzón et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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A computational interactome and functional annotation for the human proteome
eLife 5:e18715.
https://doi.org/10.7554/eLife.18715
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