Importing Network and Attribute Data into Cytoscape

Importing Network and Attribute Data into Cytoscape

12/7/2010

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Importing a Network 1. Go to File -> Import ->Network (multiple file types) 2. The Import Network File dialog box should appear 3. Under “Data Source Type”, make sure “Local” is selected

Make sure “local” is selected

Click “Select”

4. Click on the “Select” button 5. Select the appropriate file that contains your data a. For this example, open the sampleData folder and select galFiltered.sif. Click “Open” and then “Import” b. The SIF file format contains 3 columns: source, interaction type, and target. “Source” and “target” are gene/protein identifiers that are used to define nodes, while “interaction type” labels the edges connecting each pair of nodes

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Portion of Example SIF file:

6. You should now see the loaded network

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Importing Attribute Data onto a Network 1. Go to File -> Import -> Attribute from Table (Text/MS Excel)

2. The Import Attribute From Table dialog box should appear on your screen 3. Under “Data Sources”, next to “Attributes”, make sure that the “Node” radio button is selected 4. Under “Data Sources”, click the “Select File(s)” button (located to the right of the Input File box)

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Make sure “node” is selected

“Select File(s)” button

5. Select the appropriate file that contains your data a. For this example, go the sampleData folder and select galExpData.pvals 6. You will see your data show up in the Import Attribute from Table dialog box 7. Under the “Advanced” heading, select “Import Everything (Key is always ID)” a. This option tells Cytoscape to load all of your data, not just the records that match already loaded networks 8. Under the “Advanced” heading, select “Show Text File Import Options” 9. Now several more options should appear below the “Advanced” heading 10. By default, “Tab” is selected as the delimiter. Unselect “Tab” and instead select “Space” 11. Under “Attribute Names”, select “Transfer First Line Attribute Names”

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Check these boxes

Uncheck “tab” and check “space”

Check “Transfer first line as attribute names”

12. In this example, there are some duplicate column headings. To change column headings, right click on a heading. The Set Attribute Name and Type dialog box appears. You can change the column heading in this box. a. Right click on column 6 (gal1RG) to open the Set Attribute Name and Type dialog box. b. Add “pval” to the end of the column name (gal1RGpval) to distinguish this column as containing p-values. Repeat for columns 7 and 8, since they are also duplicate column titles. 13. Click “Import”

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14. The attribute data has now been loaded

15. Under the data panel, click on the Table Attributes button. Now you will see the attributes that you just loaded.

Table Attributes button

Attributes added from file

Note: For more information about the Cytoscape sample data set, see Ideker T, et al. 2001. “Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.” Science 292(5518): 929-934 Note: This handout was put together with help from documentation put together by Scooter Morris (University of California San Francisco).

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