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My inquiry pertains to WGCNA. After identifying the modules, I would like to extract genes within the different modules to create a dataframe with two columns: Gene_a and Gene_b. The values in these columns should represent co-expressed genes. An illustrative example is as follows:

enter image description here

In this example, the gene XX62730x is co-expressed with XCGR1Y. And YYYYY is co-expressed with ZZZZZZ.

However, I am facing difficulties as the official WGCNA page is no longer accessible.

I would greatly appreciate any help you can provide. Thank you in advance!

Best,
Nana

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  • $\begingroup$ The archive.org copy might help while you're trying to figure out the answer: web.archive.org/web/20231002045159/https://… $\endgroup$
    – Ram RS
    Commented Feb 5 at 17:39
  • $\begingroup$ @RamRS thanks for the link! $\endgroup$
    – nann
    Commented Feb 5 at 18:26
  • $\begingroup$ Unfortunately, the links on that link do not work. $\endgroup$
    – nann
    Commented Feb 5 at 18:31
  • $\begingroup$ I tested a couple and they worked - you need to learn to navigate archive.org to be able to leverage those links the best way. $\endgroup$
    – Ram RS
    Commented Feb 5 at 20:39
  • $\begingroup$ U can follow WGCNA R packages $\endgroup$
    – Umar
    Commented Feb 6 at 8:41

1 Answer 1

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You can get this information, more or less, using the functions exportNetworkToVisANT and exportNetworkToCytoscape. You will find some extra columns that you can ignore or delete from the resulting table. We are still working with UCLA to restore the WGCNA page including the tutorials, but the tutorials can temporarily be accessed using this dropbox link.

To use either one of the two functions, you will need the network matrix for which we usually use TOM. You will probably want to set a threshold for connections to be included, otherwise you will get a fully connected network and the resulting table will (usually) be huge.

Hope this helps!

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  • $\begingroup$ thank you very much, that really helped me $\endgroup$
    – nann
    Commented Feb 6 at 13:10

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