Tutorial 1.2 - Import modules from Biomart
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The document provides a 4 step tutorial for importing KEGG pathways from the KEGG database into Cytoscape. The steps include: 1) clicking "Import Data from KEGG" and selecting KEGG pathways, 2) leaving default options and clicking next, 3) selecting Homo sapiens and clicking next, 4) giving a name and folder location for the downloaded files which will include a file mapping genes to pathways and another with pathway annotations.
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Tutorial 1.2 - Import modules from Biomart
- 1. Tutorial 1.2: Import Pathways From KEGG Import a module file that maps human genes to KEGG pathways
- 2. STEP 1 Click Import Data from KEGG or select Import> Modules>KEGG pathways...
- 3. STEP 2 Leave default options and click Next
- 4. STEP 2 Select homo sapiens and click Next
- 5. STEP 3 Select the type of identifier for genes. This must correspond with the attribute of the rows in you data matrix. In this case since the attribute used in IntOGen matrix are Ensembl Gene IDs, we will choose this for attributes of items in the module file. Click Next.
- 6. STEP 4 Give a name to the file that will be downloaded and indicate a Folder where to place it. Click Finish.
- 7. Once the download has been completed you will have two new files in the directory that you indicated. This file is a table with the This file is a two columns file that annotations of pathway ids. For each maps the gene with the pathway id pathway id the name of the pathway is indicated.
- 8. THANKS FOR USING GITOOLS http://www.gitools.org