Abstract
SUMMARY: We present PPIXpress and PPICompare as two webservers that enable analysis of protein-protein interaction networks (PPINs). Given a reference PPIN and user-uploaded expression data from one or multiple samples, PPIXpress constructs context-dependent PPINs based on major transcripts and high-confidence domain interactions data. To derive a differential PPIN that distinguishes two groups of contextualized PPINs, PPICompare identifies statistically significant altered interactions between multiple context-dependent PPINs from PPIXpress. We present a case study where PPIXpress and PPICompare webservers were used in combination to construct the PPINs specific for melanocytic nevi and primary melanoma cells, and to detect the rewired protein interactions between these two sample types. AVAILABILITY AND IMPLEMENTATION: PPIXpress and PPICompare webservers are available at https://service.bioinformatik.uni-saarland.de/ppi-webserver/index_PPIXpress.jsp and https://service.bioinformatik.uni-saarland.de/ppi-webserver/index_PPICompare.jsp, respectively. Alternatively, the webservers and application updates can be found at https://service.bioinformatik.uni-saarland.de/ppi-webserver/.