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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.


PSA score ratios of Calcium Signaling Pathway computed with simulated data.Target nodes are: M-“MAPK signaling pathway”, P-“Phosphatidylinositol signaling system”, A-“Apoptosis”. Tissues are: “CD14_mo”-CD14 monocytes, “Adip”-Adipocytes, “Card”-Cardiac myocytes.
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f5: PSA score ratios of Calcium Signaling Pathway computed with simulated data.Target nodes are: M-“MAPK signaling pathway”, P-“Phosphatidylinositol signaling system”, A-“Apoptosis”. Tissues are: “CD14_mo”-CD14 monocytes, “Adip”-Adipocytes, “Card”-Cardiac myocytes.

Mentions: To further demonstrate necessity of tissue-specific tuning for assessment of pathway activity changes, we compared pathway flows in original and tuned KEGG Calcium Signaling Pathways with three gene expression datasets (norm vs B05 and B01) in CD14 monocytes, Adipocytes, and Cardiac myocytes (seeSupplementary Material for details). For calculations, we have used the Pathway Scoring Application for Cytoscape6. The simulations show that pathway tuning increases the sensitivity of the pathway for signal flow analysis and thus the ability of the method to detect differentially expressed gene-related changes (Figure 5).


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

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

PSA score ratios of Calcium Signaling Pathway computed with simulated data.Target nodes are: M-“MAPK signaling pathway”, P-“Phosphatidylinositol signaling system”, A-“Apoptosis”. Tissues are: “CD14_mo”-CD14 monocytes, “Adip”-Adipocytes, “Card”-Cardiac myocytes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: PSA score ratios of Calcium Signaling Pathway computed with simulated data.Target nodes are: M-“MAPK signaling pathway”, P-“Phosphatidylinositol signaling system”, A-“Apoptosis”. Tissues are: “CD14_mo”-CD14 monocytes, “Adip”-Adipocytes, “Card”-Cardiac myocytes.
Mentions: To further demonstrate necessity of tissue-specific tuning for assessment of pathway activity changes, we compared pathway flows in original and tuned KEGG Calcium Signaling Pathways with three gene expression datasets (norm vs B05 and B01) in CD14 monocytes, Adipocytes, and Cardiac myocytes (seeSupplementary Material for details). For calculations, we have used the Pathway Scoring Application for Cytoscape6. The simulations show that pathway tuning increases the sensitivity of the pathway for signal flow analysis and thus the ability of the method to detect differentially expressed gene-related changes (Figure 5).

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.