![]() ![]() In the latest Metascape release, we now propose a way to compile an integrated PPI database including STRING, BioGrid, OmniPath and InWeb_DB. All interactions in STRING has a quality score, therefore, one can prioritize and use only the high-quality subset, however, we are not able to assign similar scores to interactions not yet captured by STRING. The main reason Metascape has not included STRING is because we have not found a good way to cross compare STRING with other PPI data sources not yet included in STRING, especially we believe data sources such as OmniPath and InWeb_DB (the latter is no longer accessible to the public, therefore Metascape only uses an old snapshot) are presumably of higher quality than most STRING data. Indeed STRING is probably the most comprehensive PPI data source, therefore, tend to provide a denser and oftentimes better looking network. Regardless of its advanced PPI analysis algorithm, the results still heavily determined by the quality of its underlying PPI database.Īnalyzing the publications citing Metascape, we found many users use STRING database for PPI analysis. Such analyses are very computational intensive and cannot be easily computed even by bioinformaticians. Then taking advantage of Metascape’s functional enrichment analysis capability, it automatically assigns putative biological roles of each MCODE complex. To infer more biologically interpretable results, Metascape applies a mature complex identification algorithm called MCODE to automatically extract protein complexes embedded in such large network. Besides stating such networks are statistically significant, there is not much biologists can say about such networks. ![]() In many gene list analysis resources, PPI analysis results in a rather massy hairball network. Metascape provides a rather unique protein-protein interaction (PPI) network analysis capability. ![]()
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