Journal
JOURNAL OF PROTEOME RESEARCH
Volume 16, Issue 6, Pages 2204-2212Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.6b01066
Keywords
mass spectrometry; protein co-occurrence; pathways; computational analysis; proteomics; protein-protein interaction; protein complex
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Funding
- Concerted Research Action of Ghent University [BOF12/GOA/014]
- ERC Advanced Grant [340941]
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Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal wayS to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge. The validity of our novel method is substantiated by the extremely few pairs that can be mapped to existing knowledge based on random associations between the same set of proteins. Moreover, using literature searches and the STRING database, we were able to derive meaningful biological associations for unannotated protein pairs that were detected using our method, further illustrating that as-yet unknown associations present highly interesting targets for follow-up analysis.
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