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iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data.

Saha A, Jeon M, Tan AC, Kang J - PLoS ONE (2015)

Bottom Line: Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context).They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes.Users can visualize the subnetworks to understand the biology of the difference.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.

ABSTRACT
Pathway analyses help reveal underlying molecular mechanisms of complex biological phenotypes. Biologists tend to perform multiple pathway analyses on the same dataset, as there is no single answer. It is often inefficient for them to implement and/or install all the algorithms by themselves. Online tools can help the community in this regard. Here we present an online gene expression analytical tool called iCOSSY which implements a novel pathway-based COntext-specific Subnetwork discoverY (COSSY) algorithm. iCOSSY also includes a few modifications of COSSY to increase its reliability and interpretability. Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context). They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes. Users can visualize the subnetworks to understand the biology of the difference.

No MeSH data available.


Related in: MedlinePlus

A workflow example that uses a leukemia dataset.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4492968&req=5

pone.0131656.g003: A workflow example that uses a leukemia dataset.

Mentions: Fig 3 explains a workflow example using a leukemia dataset (AML vs. ALL) [27]. iCOSSY highlights subnetworks that are most correlated with the phenotypes. Users can explore and combine the subnetworks and construct their own networks (hypotheses) using the stitch and filter options. Finally, users can save their networks as images (e.g., PNG, SVG, and PDF) or as standard graph markup formats (e.g., XGMML, GraphML, and SIF).


iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data.

Saha A, Jeon M, Tan AC, Kang J - PLoS ONE (2015)

A workflow example that uses a leukemia dataset.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492968&req=5

pone.0131656.g003: A workflow example that uses a leukemia dataset.
Mentions: Fig 3 explains a workflow example using a leukemia dataset (AML vs. ALL) [27]. iCOSSY highlights subnetworks that are most correlated with the phenotypes. Users can explore and combine the subnetworks and construct their own networks (hypotheses) using the stitch and filter options. Finally, users can save their networks as images (e.g., PNG, SVG, and PDF) or as standard graph markup formats (e.g., XGMML, GraphML, and SIF).

Bottom Line: Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context).They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes.Users can visualize the subnetworks to understand the biology of the difference.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.

ABSTRACT
Pathway analyses help reveal underlying molecular mechanisms of complex biological phenotypes. Biologists tend to perform multiple pathway analyses on the same dataset, as there is no single answer. It is often inefficient for them to implement and/or install all the algorithms by themselves. Online tools can help the community in this regard. Here we present an online gene expression analytical tool called iCOSSY which implements a novel pathway-based COntext-specific Subnetwork discoverY (COSSY) algorithm. iCOSSY also includes a few modifications of COSSY to increase its reliability and interpretability. Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context). They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes. Users can visualize the subnetworks to understand the biology of the difference.

No MeSH data available.


Related in: MedlinePlus