= 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 '''!EntrezGene''' 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 looks like the following screenshot:
 {{attachment:importdialog1.png}}
 13. Press ''Import''.  The network has new 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 ''Annotation'' 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}}

== Create Custom Mapping/Annotation Files by Ensembl Biomart ==
[[http://www.ensembl.org/biomart/martview|Ensembl Biomart]] is a web application to create custome annotation files from variety of data sources.  You can create your own Cytoscape annotation files in few minutes by using biomart.  The following is a tutorial to create custome annotation file for a human PPI network with EntrezGene ID as node identifier.

 1. Load a human PPI network '''''Human Protein-Protein: Rual et al. (Subnetwork for tutorial)'''''.
 1. Go to [[http://www.ensembl.org/biomart/martview|Biomart web page]].
 1. Select  '''''Ensembl 45''''' as data base, then select '''''Homo sapiens genes (NCBI36)''''' as dataset.
 {{attachment:biomart1.png}}
 1. Click '''''Attributes'''''.  On the right, '''''Features''''' button is selected by default.
 1. Click '''''GENE'''''.  '''''Ensembl Gene ID''''' and '''''Ensembl Transcript ID''''' are selected.  You can select as many attributes as you need.
 1. Click '''''EXTERNAL'''''.  Select '''''EntrezGene ID'''''.  This will be used as the primary key for mapping.  Select other attributes if necessary.
 1. Click other categories and select attributes you need to import.
 1. Press '''''Result''''' button.  Now you can see the result as HTML.  (see the following)
 {{attachment:biomart2.png}}
 1. Select '''''Compressed file (.gz)''''' from the combo box menu and make sure TSV (Tab-delimited text file) is selected.
 1. Press '''''GO'''''.  Biomart will create a compressed annotation file for you.  Download process start automatically.
 1. Go back to Cytoscape window and open attribute table import dialog from '''''File-->Import-->Attribute from Table'''''.
 1. Open the gzipped file from biomart.  (Cytoscape supports compressed files, so you do not have to de-compress the file.) 
 1. Check ''Show Text File Import Options'' and click ''Transfer first line as attribute names'' checkbox.
 1. Uncheck "Show Text File Import Options'' and check ''Mapping Options''.
 1. Select '''!EntrezGene''' as '''Primary Key'''.
 1. Right-click on '''!EntrezGene''' column name and set the type to ''String''.
 {{attachment:biomart3.png}}
 1. Press ''Import''.  New attributes and IDs are mapped onto the network.