<p>I have an <code>RNA-seq</code> dataset from <code>siRNAs</code> targeting different components of a molecular pathway. the problem is that the <strong>siRNA target gene is less down-regulated from several other genes</strong>.</p>
<p><em>I'd like to know which genes are down-regulated due to the off-target effect of the siRNA and which ones are down-regulated because of the down-regulation of my target gene.</em></p>
<p>So, how can I find the <strong>off-targets</strong> of my siRNA considering having the RNA-seq data and also the siRNA sequence?</p>
<p>If there is no package in R, Python, or shell. Could you please introduce me to an online tool for finding potential off-targets using my siRNA sequence. That way I can search for off-targets and then exclude them from my DGE list manually.</p>

CC BY-SA 4.0
2020-08-21T07:51:17.737Z
The problem gets even worse when considering that two of the siRNA targets aren't even differentially down-regulated to be part of any co-expression network!!
Reza Rezaei
CC BY-SA 4.0
2020-08-21T07:53:42.840Z
about co-expression modules, what if the off-target is also in the co-expression module, how can say if the gene is an off-target or is down-regulated because of my target knockdown?
Reza Rezaei
CC BY-SA 4.0
2020-08-21T19:56:23.583Z
Nice idea @ATpoint . I don't have several siRNAs targeting same gene. But I have several siRNAs targeting different genes which their proteins aggregate to a complex! So, I guess I can somehow use this idea. I mean just check the DEGs in a heatmap and see which ones are constantly down in most of the treatment. What do you think?
Reza Rezaei
<rna-seq>
How to find siRNA off-targets from RNA-seq data?
# How to find siRNA off-targets from RNA-seq data?

(Asked by: username_0 on 2020-08-20)

I have an `RNA-seq` dataset from `siRNAs` targeting different components of a molecular pathway. the problem is that the **siRNA target gene is less down-regulated from several other genes**.

*I'd like to know which genes are down-regulated due to the off-target effect of the siRNA and which ones are down-regulated because of the down-regulation of my target gene.*

So, how can I find the **off-targets** of my siRNA considering having the RNA-seq data and also the siRNA sequence?

If there is no package in R, Python, or shell. Could you please introduce me to an online tool for finding potential off-targets using my siRNA sequence. That way I can search for off-targets and then exclude them from my DGE list manually.

**Tags:** rna-seq
> **Comments:**
> **username_0**: The problem gets even worse when considering that two of the siRNA targets aren't even differentially down-regulated to be part of any co-expression network!!  
> **username_0**: about co-expression modules, what if the off-target is also in the co-expression module, how can say if the gene is an off-target or is down-regulated because of my target knockdown?  
> **username_0**: Nice idea @ATpoint . I don't have several siRNAs targeting same gene. But I have several siRNAs targeting different genes which their proteins aggregate to a complex! So, I guess I can somehow use this idea. I mean just check the DEGs in a heatmap and see which ones are constantly down in most of the treatment. What do you think?  

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## 0 answers

