Reconstruction and comparison of cellular signaling pathway resources for the systems-level analysis of cross-talks

Abstract

Signaling pathways control a large variety of cellular processes and their defects are often linked with diseases. Reliable analyses of these pathways need uniform pathway definitions and curation rules applied to all pathways. Here, we compare KEGG, Reactome, Netpath and SignaLink pathway databases and examine their usefulness in systems-level analysis. Further on, we show that the integration of various bioinformatics databases allows a comprehensive understanding of the regulatory processes that control signaling pathways. We also discuss the drug target relevance of cross-talking (i.e., multi-pathway) proteins and signal transduction regulators (e.g., phophatases and miRNAs). Accordingly, modern integrated databases are not only essential for studying signaling processes at the systems level, but will also serve as invaluable tools for pharmacology and network-based medicine.