Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T07:51:17.737Z
Comments.Text: 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!!
Comments.UserDisplayName: Reza Rezaei
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T07:53:42.840Z
Comments.Text: 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?
Comments.UserDisplayName: Reza Rezaei
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T19:56:23.583Z
Comments.Text: 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?
Comments.UserDisplayName: Reza Rezaei
Tags: <rna-seq>
Title: How to find siRNA off-targets from RNA-seq data?
ThreadText: # 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
  
  