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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
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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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
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