How to Use Gene Name Mapping Files

This is a quick tutorial to learn how to use Gene Name Mapping files.

Import Network and Name Mapping Files

1. Download name mapping files. Mapping files are available at [http://chianti.ucsd.edu/kono/genenamemapping.html this page]. In this tutorial, we are going to use dictionary_no_prefix.zip, which is a file set without prefixes for each gene names. Unzip the archive.

2. Load sample network file. Open network import dialog from File-->Import-->Network (multiple file types)... Then click URL radio button and import Human Protein-Protein: Rual et al. (Subnetwork for tutorial).

3. Open attribute table import dialog from File-->Import-->Attribute from Table.

4. Select human.dic_cyto.txt as the input file.

5. Check "Show Text File Import Options and click Transfer first line as attribute names checkbox.

6. Uncheck "Show Text File Import Options and check Mapping Options.

7. Select EnterzGene as Primary Key.

8. Right-click on EntrezGene column name and set the type to String.

9. Do the same for HGNC.

10. Right-click on Other Aliases and select List as the data type.

11. Check Other Aliases as Alias (under "Alias?" checkboxes).

12. Now the Table Import dialog is looks like the following: attachment:importdialog1.png

13. Press Import. Now the network has the names in the text file as attributes. attachment:nameMapping1.png

Annotate Network by Gene Association File

Note: the following tutorial is for Cytoscape 2.5 beta and later.

1. Open Gene Ontology import dialog: File-->Import-->Ontology and Annotation

2. From Annotaiton menu, select Gene Association file for Homo Sapiens.

3. Click Show Mapping Options.

4. Select DB_Object_ID as Primary Key.

5. Select UniProt for Key Attribute for Network.

6. Press Import. The network is now annotated by Gene Association file! attachment:nameMapping2.png