Advanced resources are important to improve our ability to extract knowledge from high-through put datasets. Ideally, these resources should facilitate data-integration, improve accessibility, and provide novel insights. We at Thakar Lab have tackled the above requirements by developing a cloud based system that provides an interactive, pathogen-responsive, cell-specific network explorer (PathCellNet www.bio-networks.com). The PathCellNet is a compendium of gene-gene association networks inferred from genome-wide transcriptional profiles deposited in public repositories. PathCellNet offers improved accessibility of publicly available genome-wide expression profiles in a context-specific manner by integrating data from independent studies. The motivation of this tool is to infer cell-type and treatment specific networks. We tested PathCellNet on publicly available datasets of influenza infection of monocyte driven dendritic cells and A549 epithelial cells and identified robust, cell-type specific, conserved and novel gene signatures.
Katanic, D., Khan, A. and Thakar, J., 2016. PathCellNet: Cell-type specific pathogen-response network explorer. Journal of Immunological Methods. (Read paper)