BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies

To study host-pathogen interaction on the systems biology level, an extension to the previously described BiologicalNetworks system is proposed. The developed methods and data integration and querying tools allow simplifying and streamlining the process of integration of diverse experimental data types, including molecular interactions and phylogenetic classifications, genomic sequences and protein structure information, gene expression and virulence data for pathogen-related studies. The data can be integrated from the databases and user's files for both public and private use.The developed system can be used for the systems-level analysis of host-pathogen interactions, including host molecular pathways that are induced/repressed during the infections, co-expressed genes, and conserved transcription factor binding sites. Previously unknown to be associated with the influenza infection genes were identified and suggested for further investigation as potential drug targets. Developed methods and data are available through the Java application (from BiologicalNetworks program at http://www.biologicalnetworks.org webcite) and web interface (at http://flu.sdsc.edu webcite).Public health initiatives increasingly recognize the importance of the cross-scale data integration, such as mounting a data-driven risk assessment of potential pandemic outbreak in specific geographical locations or discovering novel therapeutic approaches [1-6]. For example, to facilitate the study of the Influenza infection outbreaks [7,8], it is desirable to apply the systems biology approach that requires integration of heterogeneous data from various domains of knowledge: flight paths of migrating birds, animals and humans; virological aspects, such as the efficiency with which the virus can be transmitted from the infected subject; cellular phenomena, such as interaction of viral proteins with surface receptors in the inner and outer respiratory tracts of hosts; phylogenetic properties of viral