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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.


Visualization of KEGG B Cell Receptor Signaling Pathway after parsing and automatic correction.Red arrows indicate edges created by PCP corrections, blue double arrows indicate reversed interactions, and violet dashed rectangles indicate processed group nodes.
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f2: Visualization of KEGG B Cell Receptor Signaling Pathway after parsing and automatic correction.Red arrows indicate edges created by PCP corrections, blue double arrows indicate reversed interactions, and violet dashed rectangles indicate processed group nodes.

Mentions: Parsing and corrections.Figure 2 shows the pathway parsed with CyKEGGParser with automatic correction options applied. These include three cases of protein-compound-protein (PCP) interaction processing, reversing binding interaction directions of seven edges and processing of two group nodes.


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

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

Visualization of KEGG B Cell Receptor Signaling Pathway after parsing and automatic correction.Red arrows indicate edges created by PCP corrections, blue double arrows indicate reversed interactions, and violet dashed rectangles indicate processed group nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Visualization of KEGG B Cell Receptor Signaling Pathway after parsing and automatic correction.Red arrows indicate edges created by PCP corrections, blue double arrows indicate reversed interactions, and violet dashed rectangles indicate processed group nodes.
Mentions: Parsing and corrections.Figure 2 shows the pathway parsed with CyKEGGParser with automatic correction options applied. These include three cases of protein-compound-protein (PCP) interaction processing, reversing binding interaction directions of seven edges and processing of two group nodes.

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.