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We achieved this by establishing a direct correspondence between individual protein interactions and underlying domain interactions in a complete but condition-unspecific protein interaction network. This knowledge was then used to infer the condition-specific presence of interactions from the dominant protein isoforms. When we compared contextualized interaction networks of matched normal and tumor samples in breast cancer, our transcript-based construction identified more significant alterations that affected proteins associated with cancerogenesis than a method that only uses gene expression data. The approach is provided as the user-friendly tool PPIXpress.<\/jats:p><jats:p>Availability and implementation: PPIXpress is available at https:\/\/sourceforge.net\/projects\/ppixpress\/.<\/jats:p><jats:p>Contact: \u00a0volkhard.helms@bioinformatik.uni-saarland.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv620","type":"journal-article","created":{"date-parts":[[2015,10,28]],"date-time":"2015-10-28T02:38:45Z","timestamp":1445999925000},"page":"571-578","source":"Crossref","is-referenced-by-count":22,"title":["PPIXpress: construction of condition-specific protein interaction networks based on transcript expression"],"prefix":"10.1093","volume":"32","author":[{"given":"Thorsten","family":"Will","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics and"},{"name":"2 Graduate School of Computer Science, Saarland University, Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Volkhard","family":"Helms","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,10,27]]},"reference":[{"key":"2023020110323870600_btv620-B1","doi-asserted-by":"crossref","first-page":"e1003632","DOI":"10.1371\/journal.pcbi.1003632","article-title":"Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases","volume":"10","author":"Barshir","year":"2014","journal-title":"PLoS Comput. 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