Answers.Body: <p>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 <a href="https://www.dropbox.com/scl/fo/4vqfiysan6rlurfo2pbnk/h?rlkey=3za224679kv8ulbpl5s9mwrkt&amp;dl=0" rel="nofollow noreferrer">this dropbox link</a>.</p>
  <p>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.</p>
  <p>Hope this helps!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-06T13:10:12.240Z
Answers.Text: thank you very much, that really helped me
Answers.UserDisplayName: nann
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-06T10:25:10.110Z
Answers.LastActivityDate: 2024-02-06T10:25:10.110Z
Answers.UserDisplayName: Peter Langfelder
Body: <p>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: <code>Gene_a</code> and <code>Gene_b</code>. The values in these columns should represent co-expressed genes. An illustrative example is as follows:</p>
  <p><a href="https://i.sstatic.net/WyULL.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/WyULL.png" alt="enter image description here" /></a></p>
  <p>In this example, the gene <code>XX62730x</code> is co-expressed with <code>XCGR1Y</code>. And <code>YYYYY</code> is co-expressed with <code>ZZZZZZ</code>.</p>
  <p>However, I am facing difficulties as the official WGCNA page is no longer accessible.</p>
  <p>I would greatly appreciate any help you can provide. Thank you in advance!</p>
  <p>Best,<br />
  Nana</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-05T17:39:56.870Z
Comments.Text: The archive.org copy might help while you're trying to figure out the answer: https://web.archive.org/web/20231002045159/https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-05T18:26:26.980Z
Comments.Text: @RamRS thanks for the link!
Comments.UserDisplayName: nann
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-05T18:31:03.513Z
Comments.Text: Unfortunately, the links on that link  do not work.
Comments.UserDisplayName: nann
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-05T20:39:05.207Z
Comments.Text: 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.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-06T08:41:18.747Z
Comments.Text: U can follow WGCNA R packages
Comments.UserDisplayName: Umar
Tags: <r><rna-seq><wgcna>
Title: WGCNA: Extract genes within the different modules to create a dataframe with two columns
ThreadText: # WGCNA: Extract genes within the different modules to create a dataframe with two columns
  
  (Asked by: username_0 on 2024-02-05)
  
  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](https://i.sstatic.net/WyULL.png)](https://i.sstatic.net/WyULL.png)
  
  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
  
  **Tags:** r, rna-seq, wgcna
  
  > **Comments:**
  > **username_1**: The archive.org copy might help while you're trying to figure out the answer: https://web.archive.org/web/20231002045159/https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/  
  > **username_0**: @username_1 thanks for the link!  
  > **username_0**: Unfortunately, the links on that link  do not work.  
  > **username_1**: 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.  
  > **username_2**: U can follow WGCNA R packages  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2024-02-06. Score: 1 | Accepted answer
  
  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](https://www.dropbox.com/scl/fo/4vqfiysan6rlurfo2pbnk/h?rlkey=3za224679kv8ulbpl5s9mwrkt&dl=0).
  
  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!
  
  > **Comments:**
  > **username_0**: thank you very much, that really helped me  
  
  ---
  
  