Clustering of gene sets within Enrichment Map

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Shawn Cho

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Apr 19, 2017, 7:13:35 PM4/19/17
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Hello,

I am trying to reproduce figures 3 and 4 of the Enrichment Map Paper with an RNAseq dataset. I've pulled out the top 1500 genes, based on magnitude of fold change and inserted them into DAVID. Following the DAVID Enrichment Map tutorial, I was able to output the nodes, but not achieve the clustering among the nodes. 

Can you specify which plugins are needed to re-create figures 3 and 4, and whether DAVID analysis is all I need?

Thanks,

Shawn


Ruth Isserlin

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Apr 20, 2017, 9:11:37 AM4/20/17
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Hi Shawn, 
The annotations of Figure 3 and 4 from that publication were done manually. We have created an app to this automatically but it won’t be the exact same as the figure. To annotate your network automatically you can use the Autoannotate app (http://apps.cytoscape.org/apps/autoannotate)  it requires a few other apps so easiest is to install the enrichment map collection http://apps.cytoscape.org/apps/enrichmentmappipelinecollection which contains all the app you need to create,and annotate an enrichment map.

For how to use auto annotate you can find the user manual here:

Thanks, 
Ruth 


 
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Shawn Cho

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Apr 26, 2017, 12:29:28 PM4/26/17
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Great! Thank you. I will probably end up using Layout > yFiles > Organic, then drawing the circles manually.

One other question - for the DAVID analysis, how does Cytoscape know which columns from 'Estrogen_expression_file.txt' map to which condition? I'm trying to incorporate this file to my enrichment map so that the map can color the up/down regulated node borders accordingly, but all my node borders are the same width.


Thanks!

Shawn

On Thursday, April 20, 2017 at 6:11:37 AM UTC-7, risserlin wrote:
Hi Shawn, 
The annotations of Figure 3 and 4 from that publication were done manually. We have created an app to this automatically but it won’t be the exact same as the figure. To annotate your network automatically you can use the Autoannotate app (http://apps.cytoscape.org/apps/autoannotate)  it requires a few other apps so easiest is to install the enrichment map collection http://apps.cytoscape.org/apps/enrichmentmappipelinecollection which contains all the app you need to create,and annotate an enrichment map.

For how to use auto annotate you can find the user manual here:

Thanks, 
Ruth 


On Apr 19, 2017, at 7:13 PM, Shawn Cho <grand...@gmail.com> wrote:

Hello,

I am trying to reproduce figures 3 and 4 of the Enrichment Map Paper with an RNAseq dataset. I've pulled out the top 1500 genes, based on magnitude of fold change and inserted them into DAVID. Following the DAVID Enrichment Map tutorial, I was able to output the nodes, but not achieve the clustering among the nodes. 

Can you specify which plugins are needed to re-create figures 3 and 4, and whether DAVID analysis is all I need?

Thanks,

Shawn



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Ruth Isserlin

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Apr 26, 2017, 1:55:55 PM4/26/17
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Hi Shawn, 
Cytoscape does not know which condition each node is mapped to with David results.  The assumption is that you have run DAVID with a set of genes (i.e. all significantly upregulated genes from your data) so all sets returned are affiliated with up-regulation.  There is no place in the DAVID output file to indicate the condition.

With other methods that use a generic enrichment results file (like gprofiler)  there is a "phenotype" column where you can affiliate the set with up or down condition and merge two analyses in the same file so you represent both conditions in the same enrichment map.  

For DAVID you could run one analysis with the up regulated genes and save the enrichment results, then run DAVID with the down regulated genes and save the enrichment results.  You can then create a two dataset enrichment map where dataset1 is the enrichment result from the up set analysis and the dataset2 is the enrichment result from the down set analysis.  In this case the centre of the node would be colored according to the up set and the border would be colored according to the down set. 

Ruth 





On Wed, Apr 26, 2017 at 12:29 PM, Shawn Cho <grand...@gmail.com> wrote:
Great! Thank you. I will probably end up using Layout > yFiles > Organic, then drawing the circles manually.

One other question - for the DAVID analysis, how does Cytoscape know which columns from 'Estrogen_expression_file.txt' map to which condition? I'm trying to incorporate this file to my enrichment map so that the map can color the up/down regulated node borders accordingly, but all my node borders are the same width.


Thanks!

Shawn

On Thursday, April 20, 2017 at 6:11:37 AM UTC-7, risserlin wrote:
Hi Shawn, 
The annotations of Figure 3 and 4 from that publication were done manually. We have created an app to this automatically but it won’t be the exact same as the figure. To annotate your network automatically you can use the Autoannotate app (http://apps.cytoscape.org/apps/autoannotate)  it requires a few other apps so easiest is to install the enrichment map collection http://apps.cytoscape.org/apps/enrichmentmappipelinecollection which contains all the app you need to create,and annotate an enrichment map.

For how to use auto annotate you can find the user manual here:

Thanks, 
Ruth 


On Apr 19, 2017, at 7:13 PM, Shawn Cho <grand...@gmail.com> wrote:

Hello,

I am trying to reproduce figures 3 and 4 of the Enrichment Map Paper with an RNAseq dataset. I've pulled out the top 1500 genes, based on magnitude of fold change and inserted them into DAVID. Following the DAVID Enrichment Map tutorial, I was able to output the nodes, but not achieve the clustering among the nodes. 

Can you specify which plugins are needed to re-create figures 3 and 4, and whether DAVID analysis is all I need?

Thanks,

Shawn



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Shawn Cho

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Apr 26, 2017, 7:57:53 PM4/26/17
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Hi Ruth,

Thanks so much for your prompt responses. I got the graph that I wanted, thanks to you!

Best,

Shawn
Shawn
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