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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.


KEGG B cell signaling pathway tuned in CD19 B cells and CD4 T cells.Tuning was performed with 25 percentile threshold of gene expression values for each tissue. Highlighted in yellow are the nodes (“LYN” and “CD19”) not present in the pathway tuned in CD4 T cells.
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f3: KEGG B cell signaling pathway tuned in CD19 B cells and CD4 T cells.Tuning was performed with 25 percentile threshold of gene expression values for each tissue. Highlighted in yellow are the nodes (“LYN” and “CD19”) not present in the pathway tuned in CD4 T cells.

Mentions: Tissue-specific tuning. We performed B Cell Receptor Signaling Pathway tuning in CD19 B cells and CD4 T cells. Gene expression threshold was set to 25 percentile of gene expression values in the dataset. After tuning, from the 57 nodes available in the original pathway, 54 nodes remained in B cells and 52 nodes remained in T cells. Two nodes, namely, LYN, and CD19 are missing in the B Cell Receptor Signaling Pathway tuned in T cells (Figure 3). Due to their topological importance in signal propagation from the receptors to the target nodes, absence of these two nodes leads to almost complete deactivation of the entire pathway in T cells.


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

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

KEGG B cell signaling pathway tuned in CD19 B cells and CD4 T cells.Tuning was performed with 25 percentile threshold of gene expression values for each tissue. Highlighted in yellow are the nodes (“LYN” and “CD19”) not present in the pathway tuned in CD4 T cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: KEGG B cell signaling pathway tuned in CD19 B cells and CD4 T cells.Tuning was performed with 25 percentile threshold of gene expression values for each tissue. Highlighted in yellow are the nodes (“LYN” and “CD19”) not present in the pathway tuned in CD4 T cells.
Mentions: Tissue-specific tuning. We performed B Cell Receptor Signaling Pathway tuning in CD19 B cells and CD4 T cells. Gene expression threshold was set to 25 percentile of gene expression values in the dataset. After tuning, from the 57 nodes available in the original pathway, 54 nodes remained in B cells and 52 nodes remained in T cells. Two nodes, namely, LYN, and CD19 are missing in the B Cell Receptor Signaling Pathway tuned in T cells (Figure 3). Due to their topological importance in signal propagation from the receptors to the target nodes, absence of these two nodes leads to almost complete deactivation of the entire pathway in T cells.

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.