Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.

ABSTRACT: Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). Both the experimental setup and the nature of PHIs exhibit certain characteristics. First, besides an environmental change, the battle between pathogen and host leads to a constantly changing environment and thus complex gene expression patterns. Second, there might be a delay until one of the organisms reacts. Third, toward later time points only one organism may survive leading to missing gene expression data of the other organism. Here, we account for PHI characteristics by extending NetGenerator, a network inference tool that predicts gene regulatory networks from gene expression time series data. We tested multiple modelin

SUBMITTER: Schulze S 

PROVIDER: S-EPMC4319478 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature