CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows

F1000Res. 2014 Jul 1;3:145. doi: 10.12688/f1000research.4410.2. eCollection 2014.


The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app ( for Cytoscape 3 that allows manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissue- and protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways.

Grant support

This study was funded by research grant from the State Committee of Science of the Ministry of Education and Science of the Republic of Armenia, granted to Arsen Arakelyan (N 13Y-1F0022, PI: AA).