Background
Macrophages are distributed in peripheral tissues where they eliminate invading exogenous substances and are therefore responsible for innate immunity. They trigger acquired immunity by capturing exogenous antigens engulfing them in cellular lysosomes. Significant progress has been made recently in understanding the biochemical mechanisms by which lopopolysaccharide (LPS) activates immune cells, particularly macrophages by analyzing quantitative microarray time course data. Unfortunately, there is no useful knowledge-base dedicated to compile the information of macrophage signal transduction pathway and their dynamics.
Description
In order to aid immunologists quest for an effective septic shock treatment, we present the first database that is specifically focused on LPS-induced macrophage signaling pathways, namely Simulatable Macrophage Pathway Knowledgebase (MACPAK). MACPAK contains 230 pathways for more than 200 genes derived from > 1000 reports which can be freely accessed by a web interface. Moreover, the information contained in the MACPAK can be easily exported to Cell System Markup Language (CSML) format and imported by Cell Illustrator for visualization as well as pathway simulation. The overview of the MACPAK contents can be accessed here. The curation manual for this project is given in here.
Conclusion
By using MACPAK, the users can study not only the topology of the pathway but also capture the dynamic behavior of the network that was described in the literature. Moreover, starting from those template models, one can develop customized models by modeling and simulation using Cell Illustrator. All macrophage template models stored in MACPAK are freely available at http://macrophagedb.csml.org and can be exported in the following formats: Cell System Markup Language (CSML), Cell System Ontology (CSO). Addtionally, via a custom Cytoscape with our CSML loader plugin, export to many other formats, e.g. Graph Modeling Language (GML), eXtensible Graph Markup Modeling Language (XGMML) and SIF are also available.
