# PPIXpress and PPICompare webservers infer condition-specific and differential PPI networks

## TL;DR

The paper introduces two web tools, PPIXpress and PPICompare, that help analyze how protein interactions change under different biological conditions.

## Contribution

The novelty lies in providing web-based tools to infer condition-specific and differential protein–protein interaction networks using expression data.

## Key findings

- PPIXpress builds context-dependent PPINs using expression data and domain interaction data.
- PPICompare identifies statistically significant interaction changes between different PPINs.
- A case study demonstrated the tools' ability to detect rewired interactions in melanocytic nevi versus melanoma cells.

## Abstract

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.

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/.