General Information
| Description | Construction of condition-specific protein interaction networks based on transcript expression |
| Homepage | https://sourceforge.net/projects/ppixpress/ |
Publications
PPIXpress: construction of condition-specific protein interaction networks based on transcript expression
Summary:
Protein–protein interaction networks are an important component of modern systems biology. Yet, comparatively few efforts have been made to tailor their topology to the actual cellular condition being studied. Here, we present a network construction method that exploits expression data at the transcript-level and thus reveals alterations in protein connectivity not only caused by differential gene expression but also by alternative splicing. 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.
Availability and implementation:
PPIXpress is available at https://sourceforge.net/projects/ppixpress/.
Contact:
volkhard.helms@bioinformatik.uni-saarland.de
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
CNAmet
Published January 2011
An R package for integrating copy number, methylation and expression data
SAPIN
Published September 2012
A framework for the structural analysis of protein interaction networks
SiPAN
Published March 2015
Simultaneous prediction and alignment of protein–protein interaction networks
BMRF-Net
Published March 2015
A software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
XLinkDB 2.0
Published April 2016
Integrated, large-scale structural analysis of protein crosslinking data
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
