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

Abstract

BackgroundUnderstanding of immune response mechanisms of pathogen-infected host requires multi-scale analysis of genome-wide data. Data integration methods have proved useful to the study of biological processes in model organisms, but their systematic application to the study of host immune system response to a pathogen and human disease is still in the initial stage.ResultsTo 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.ConclusionsThe 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) and web interface (at http://flu.sdsc.edu).

Integration and visualization of host–pathogen data related to infectious diseases

“…CDC (www.cdc.gov), WHO (www.who.int) and HealthMap (healthmap.org)], yet they mainly focus on epidemiological information and provide little or no host or pathogen data. Some resources, such as BiologicalNetworks, PHIDIAS, PHI-base and PIG, integrate host-pathogen interactions at different levels, but lack disease or outbreak information (Driscoll et al, 2009;Kozhenkov et al, 2011;Winnenburg et al, 2008;Xiang et al, 2007). These are a few recent examples of attempts to integrate different types of host, pathogen and disease information; a comprehensive review is beyond the scope of this article.…”

Interactive exploration of integrated biological datasets using context-sensitive workflows

“…Currently, the qualitative assessment requires in-depth expert knowledge about the components in the network model and about its dependence upon the experimental setting. Online resources providing static, pre-integrated knowledge, such as BiologicalNetworks (Kozhenkov et al, 2011 ) and GeneMania (Mostafavi et al, 2008 ), focus on widely-studied model organisms or require the upload of experimental in-house data. With the increasing number of sequenced organisms, we predict a further diversification of studied organisms and an increased need to create custom integration networks.…”

An Integrative Approach to Inferring Gene Regulatory Module Networks

“…The modules, search, analysis and visualization capabilities are described in detail in the authors’ earlier works [21], [22], [23].…”

“…The resource relies on the database IntegromeDB, which integrates public data on gene expression, pathways, gene and protein sequences from multiple species, and contains a comprehensive collection of public data on TF binding sites and gene regulatory sequences [20]. This database is accessible within the BiologicalNetworks application that has been developed by the authors to provide integrative analysis and visualization of networks, microarrays, and sequences [21], [22]. In this work, BiologicalNetworks was extended with tools for inferring and analysis of gene regulatory modules and networks.…”