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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.


Web interface.The most common scenario involves a user uploading a gene-expression file, a class-label file, and if necessary a chip file, and then clicking the “Analyze & Explore” button to get the results. The website provides the user a link that shows the results once the analysis is completed.
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pone.0131656.g002: Web interface.The most common scenario involves a user uploading a gene-expression file, a class-label file, and if necessary a chip file, and then clicking the “Analyze & Explore” button to get the results. The website provides the user a link that shows the results once the analysis is completed.

Mentions: We have newly developed a web server called iCOSSY, available at http://icossy.korea.ac.kr. Here, users can upload their own gene expression profile datasets along with known labels, and can identify the important subnetworks differentially expressed between the labels. The web interface is shown in Fig 2. Network visualization is important for generating new hypotheses. Users can interactively visualize subnetworks returned by iCOSSY analysis (see Fig 1). They can view networks as separate entities or as a whole. iCOSSY automatically stitches multiple subnetworks using KEGG, STRING, or Pathway API. The nodes (genes) are colored according to their expression patterns. Users can also freely edit graphs and save networks for later use.


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

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

Web interface.The most common scenario involves a user uploading a gene-expression file, a class-label file, and if necessary a chip file, and then clicking the “Analyze & Explore” button to get the results. The website provides the user a link that shows the results once the analysis is completed.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131656.g002: Web interface.The most common scenario involves a user uploading a gene-expression file, a class-label file, and if necessary a chip file, and then clicking the “Analyze & Explore” button to get the results. The website provides the user a link that shows the results once the analysis is completed.
Mentions: We have newly developed a web server called iCOSSY, available at http://icossy.korea.ac.kr. Here, users can upload their own gene expression profile datasets along with known labels, and can identify the important subnetworks differentially expressed between the labels. The web interface is shown in Fig 2. Network visualization is important for generating new hypotheses. Users can interactively visualize subnetworks returned by iCOSSY analysis (see Fig 1). They can view networks as separate entities or as a whole. iCOSSY automatically stitches multiple subnetworks using KEGG, STRING, or Pathway API. The nodes (genes) are colored according to their expression patterns. Users can also freely edit graphs and save networks for later use.

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.