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

Abstract (Expand)

The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app ( http://apps.cytoscape.org/apps/cykeggparser) 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.

Authors: L. Nersisyan, R. Samsonyan, A. Arakelyan

Date Published: 13th Nov 2014

Publication Type: Journal

KEGGParser: parsing and editing KEGG pathway maps in Matlab.

Abstract (Expand)

SUMMARY: KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required … information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab. AVAILABILITY AND IMPLEMENTATION: The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

Authors: A. Arakelyan, L. Nersisyan

Date Published: 15th Feb 2013

Publication Type: Journal

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