Answers.Body: <p>This is a a symmetric matrix with the pathways in both axes. So for each pair a similarity index is calculated (usually it takes into account the number of genes in each pathway and the total number of genes in both pathways). There are several similarity indexes available. A typical one is <a href="https://en.wikipedia.org/wiki/Jaccard_index" rel="nofollow noreferrer">Jaccard</a> or <a href="https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient" rel="nofollow noreferrer">Sørensen-Dice</a> index, usually 0 means no similarity and 1 equal pathways.</p>
  
  <p>You can do this kind of analysis in R using <a href="https://bioconductor.org/packages/BioCor/" rel="nofollow noreferrer">BioCor</a> (Disclosure: I am the author of this package) which uses the Dice similarity. You will need the name of the genes of each pathway, after calculating the similarity of pathways using <code>mpathSim</code>, you can then plot it with a heatmap (using the <code>heatmap</code> function).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-29T08:59:29.903Z
Answers.Text: yes i remember  from my last post you have given the link im going to use it and let you know ..i think this looks bit more comprehensive to put all the pathway together..if i have any issue with your library i will ask you..
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-29T08:44:27.873Z
Answers.LastActivityDate: 2019-01-29T08:44:27.873Z
Answers.UserDisplayName: llrs
Body: <p>So I'm doing a pathway analysis using <a href="https://genetrail2.bioinf.uni-sb.de/start.html" rel="nofollow noreferrer">GeneTrail</a> database. One thing I am not able to get is this similarity measure being calculated and plotted: </p>
  
  <p><a href="https://i.sstatic.net/cG2f7.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cG2f7.jpg" alt="figure"></a></p>
  
  <p>I want to know how this is being made, what is the output being plotted because each gene is may be involved in multiple pathways.</p>
  
  <p>I want to be able to make it in R again. Any suggestion or help would be appreciated. How to plot the enrichment result in this form ?</p>
  
Tags: <r><rna-seq><pathway><figure-explanation>
Title: Pathway plot in GeneTrail data base
ThreadText: # Pathway plot in GeneTrail data base
  
  (Asked by: username_0 on 2019-01-29)
  
  So I'm doing a pathway analysis using [GeneTrail](https://genetrail2.bioinf.uni-sb.de/start.html) database. One thing I am not able to get is this similarity measure being calculated and plotted:
  
  [![figure](https://i.sstatic.net/cG2f7.jpg)](https://i.sstatic.net/cG2f7.jpg)
  
  I want to know how this is being made, what is the output being plotted because each gene is may be involved in multiple pathways.
  
  I want to be able to make it in R again. Any suggestion or help would be appreciated. How to plot the enrichment result in this form ?
  
  **Tags:** r, rna-seq, pathway, figure-explanation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-01-29. Score: 3 | Accepted answer
  
  This is a a symmetric matrix with the pathways in both axes. So for each pair a similarity index is calculated (usually it takes into account the number of genes in each pathway and the total number of genes in both pathways). There are several similarity indexes available. A typical one is [Jaccard](https://en.wikipedia.org/wiki/Jaccard_index) or [Sørensen-Dice](https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient) index, usually 0 means no similarity and 1 equal pathways.
  
  You can do this kind of analysis in R using [BioCor](https://bioconductor.org/packages/BioCor/) (Disclosure: I am the author of this package) which uses the Dice similarity. You will need the name of the genes of each pathway, after calculating the similarity of pathways using `mpathSim`, you can then plot it with a heatmap (using the `heatmap` function).
  
  > **Comments:**
  > **username_0**: yes i remember  from my last post you have given the link im going to use it and let you know ..i think this looks bit more comprehensive to put all the pathway together..if i have any issue with your library i will ask you..  
  
  ---
  
  