<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>

CC BY-SA 4.0
2024-02-06T13:10:12.240Z
thank you very much, that really helped me
nann
CC BY-SA 4.0
2024-02-06T10:25:10.110Z
2024-02-06T10:25:10.110Z
Peter Langfelder
<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>

CC BY-SA 4.0
2024-02-05T17:39:56.870Z
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/
Ram RS
CC BY-SA 4.0
2024-02-05T18:26:26.980Z
@RamRS thanks for the link!
nann
CC BY-SA 4.0
2024-02-05T18:31:03.513Z
Unfortunately, the links on that link  do not work.
nann
CC BY-SA 4.0
2024-02-05T20:39:05.207Z
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.
Ram RS
CC BY-SA 4.0
2024-02-06T08:41:18.747Z
U can follow WGCNA R packages
Umar
<r><rna-seq><wgcna>
WGCNA: Extract genes within the different modules to create a dataframe with two columns
# 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**: @RamRS 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  

---

