Generating gene network from only a list of genes

[Douglas Cavener]

I'm a newbie to Cytoscape and have a very simple application; I want to take a list of 78 genes that were identified as being highly diverged in one mammalian species relative to other mammals and generate a gene network among the 78 genes. In this case it is appropriate to use the human Bio-Grid. So I upload the human Bio-Grid and then I attempted to upload my gene list ( Excel doc) using "Import Table"; however I received an error message that I must have more than one data column (and I don't because I just have a single column with my 78 gene names). I was assuming the Cytoscape could take my limited gene list and use the human Bio-Grid to generate a gene network among my gene set. Any suggestions would be appreciated. Thanks! Doug

[Michael G]

Hi Doug,
There are 2 options I am aware of:
1. Add-on Cypath2 - AdvancedQuery:
Here you can paste in your genes of interest and search for known interactions/connections to other proteins, complexes,...

2. Table-import + Filtering:
If you only want to import & visualize your genes of interest, simply generate a 2-column file (tab-delimited .txt, .csv, .xlsx., ....). The first column contains your gene identifiers that match your network (you can use the add-on BridgeDB to add more identifiers like RefSeq, Ensembl, ...), the second one contains any value (i.e. "1")
Then you import your table and assign the given value to your network. You can now filter (tab "Select") for this column to visualize your genes of interest.
You might even modify the Style of the Network to colorize any nodes which contain the "1" in your desired column.

Hope that answered your question.

Michael