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Enrichment Map Analysis Using Cytosscape

1. Enrichment analysis using DAVID

a. Google for “david nih” and select the first hit to go to DAVID enrichment analysis tool;

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b. At the DAVID homepage, click the “Functional Annotation” tab and copy/paste your gene name list in the Step 1 box, Select “Official Gene Symbol” for Step 2, Select “Gene List” for Step 3 and click “Submit”....

 

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c. In the resulting window, click “Homo sapiens” and click the “Select Species” button and Click the “Functional Annotation Chart”. Download the resulting file p49CDY9mfDuKGIYpQL5pbIBmojW1gDhdbTMJ2UwefYl5KbTrUauDOUJGmvNprheC1Ci4HwIvObCNkpUMZ6AcBE94BkGsCkwlxyDCH4s2TNmBbdlLr9Cu21-FDijb9kqh7mF5hx8V.


2. Enrichment Map

2.1. Install cytoscape plugins

a. Start Cytoscape and install AutoAnnotate, EnrichmentMap plugins. Start the EnrichmentMap plugin from the Apps menu. Select the following as the options for the EnrichmentMap and click “Build”.

 

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2.2. Adjust the thresholds

a. Adjust the p-value and q-value to the maximum of 1.

b. Run the AutoAnnotate App to cluster and identify common themes in the data. Also run the WordCloud App to visualize pattern

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