PPI spider: A tool for the interpretation of proteomics data in the context of protein-protein interaction networks

Alexey V. Antonov, Sabine Dietmann, Igor Rodchenkov, Hans W. Mewes

Research output: Contribution to journalArticlepeer-review

62 Scopus citations

Abstract

Recent advances in experimental technologies allow for the detection of a complete cell proteome. Proteins that are expressed at a particular cell state or in a particular compartment as well as proteins with differential expression between various cells states are commonly delivered by many proteomics studies. Once a list of proteins is derived, a major challenge is to interpret the identified set of proteins in the biological context. Protein-protein interaction (PPI) data represents abundant information that can be employed for this purpose. However, these data have not yet been fully exploited due to the absence of a methodological framework that can integrate this type of information. Here, we propose to infer a network model from an experimentally identified protein list based on the available information about the topology of the global PPI network. We propose to use a Monte Carlo simulation procedure to compute the statistical significance of the inferred models. The method has been implemented as a freely available web-based tool, PPI spider (http://mips.helmholtz-muenchen.de/proj/ppispider). To support the practical significance of PPI spider, we collected several hundreds of recently published experimental proteomics studies that reported lists of proteins in various biological contexts. We reanalyzed them using PPI spider and demonstrated that in most cases PPI spider could provide statistically significant hypotheses that are helpful for understanding of the protein list.

Original languageEnglish
Pages (from-to)2740-2749
Number of pages10
JournalProteomics
Volume9
Issue number10
DOIs
StatePublished - May 2009

Keywords

  • Enrichment analyses
  • Inference of molecular mechanisms that are relevant to a given protein list
  • Protein-protein interaction networks

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