Molecular Interaction Map of a Macrophage

Kanae Oda,1-3 Tomomi Kimura,1,3 Yukiko Matsuoka,4 Akira Funahashi,4 Masaaki Muramatsu,3 and Hiroaki Kitano1,2,5

1.  The Systems Biology Institute, Tokyo, Japan

2.  Department of Fundamental Science and Technology, Keio University

3.  Dept. Molecular Epidemiology, Medical Research Institute. Tokyo Medical and Dental University, Tokyo, Japan

4.  ERATO-SORST Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Tokyo, Japan

5.  Sony Computer Science Laboratory, Inc., Tokyo, Japan

KO and TK contributed equally to this paper.

Abstract

Identifying intracellular molecular interactions is the first step toward understanding complex dynamics and mechanisms of the cell. We have created a comprehensive map of molecular interactions in a macrophage based on published literature. The map was created to analyze the experimental data sets produced by the Alliance for Cellular Signaling (AfCS). Therefore, we have extensively focused on signal transduction pathways that are targeted by the AfCS and have included essential metabolism, transcription, and secretion pathways that may be relevant. The map was created using CellDesigner, a software we have developed for molecular interaction map construction, and represented in Systems Biology Markup Language (SBML). This report describes notations used in the interaction map and the main features of CellDesigner and provides a list of all published literature that has been referenced in creating version 1.0 of the map.