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

Nersisyan L, Samsonyan R, Arakelyan A - F1000Res (2014)

Bottom Line: The KEGG pathway database is a widely accepted source for biomolecular 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.

View Article: PubMed Central - PubMed

Affiliation: Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan, 0014, Armenia.

ABSTRACT
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.

No MeSH data available.


Graphical representation of CyKEGGParser use case.
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Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4215754&req=5

f1: Graphical representation of CyKEGGParser use case.

Mentions: The software is implemented in Java and is available as an app for Cytoscape 3. The general workflow of CyKEGGParser is presented inFigure 1.


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

Nersisyan L, Samsonyan R, Arakelyan A - F1000Res (2014)

Graphical representation of CyKEGGParser use case.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4215754&req=5

f1: Graphical representation of CyKEGGParser use case.
Mentions: The software is implemented in Java and is available as an app for Cytoscape 3. The general workflow of CyKEGGParser is presented inFigure 1.

Bottom Line: The KEGG pathway database is a widely accepted source for biomolecular 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.

View Article: PubMed Central - PubMed

Affiliation: Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan, 0014, Armenia.

ABSTRACT
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.

No MeSH data available.