Functional gene clustering - regarding

[Bharani Dharan]

Hi there,

             I am new to cytoscape and networking. I have a dataset of KEGG ortholog (KO) numbers and their abundance (Gene count) for each of my samples. How can I construct a gene network and identify the cluster of gene contributing for a specific function? What kind of app, data and data format do I need? Thanks in advance.

[Scooter Morris]

Hi Bharani,

   Welcome to Cytoscape!  Well, the first problem is to convert your KO numbers to a more recognized identifier such an UniProt, HGNC, or Ensembl.  Then, you could use STRING to create a protein-protein interaction network and add your gene counts to that.  Once that is done, there are a number of approaches to functionally annotate that network with GO or KEGG and then do your clustering to see what kinds of enrichment you have.  So, I would suggest you start with the stringApp, which will allow you to enter a gene list (your converted KO numbers) and give you a network.  Then do an Import Table to merge in your abundance, and finally use the stringApp to do enrichment, clusterMaker2 to cluster your network (look at the MCL algorithm), then maybe EnrichmentMap to visualize what kind of functions you have...

But, at the end of the day, you'll need to convert those KO numbers to something else.  As far as file formats, I would just create a spreadsheet with your KO numbers in a column, the corresponding UniProt identifiers in a column, and your counts in another column.  That should get you started....

-- scooter

[Bharani Dharan]

Dear Mr.Scooter,

            Thanks a lot for your kind response. I will proceed accordingly. 

With thanks,

R.Bharanidharan

வெள்., 14 செப்., 2018, முற்பகல் 12:17 அன்று, Scooter Morris <ssbsm...@gmail.com> எழுதியது:

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