Enrichment Map doesn't work well in Cytoscape

[rosafontana]

Hi,

I'm trying to use Enrichment Map in Cytoscape to analyze GOBP and Reactome data that I downloaded from g:Profile. I have a MacBook Pro 2020 Processor: 2 GHz Quad-Core Intel Core i5 Memory : 16 GB 3733 MHz LPDDR4X

When I start to run the analysis the computer fans go on and the process is really slow. Today I was finally able to see the map but when I tried to click on the nodes Cytoscape stops to work and I need to force the quit. Can you help me with this issue?

If you need: Cytoscape version: 3.8.2 Java: 11.0.6 by AdoptOpenJDK Enrichment Map version: 3.3.3.

Thanks

[veroniquevoisin]

Hi, how many nodes do you have once the map is created? Did you upload a gmt file while creating the enrichment map (the gmt file should not be put in the input box but on the right field only)? veronique

On Tue, Sep 21, 2021 at 7:21 PM rosafontana @.***> wrote:

Hi,

I'm trying to use Enrichment Map in Cytoscape to analyze GOBP and Reactome data that I downloaded from g:Profile. I have a MacBook Pro 2020 Processor: 2 GHz Quad-Core Intel Core i5 Memory : 16 GB 3733 MHz LPDDR4X

When I start to run the analysis the computer fans go on and the process is really slow. Today I was finally able to see the map but when I tried to click on the nodes Cytoscape stops to work and I need to force the quit. Can you help me with this issue?

If you need: Cytoscape version: 3.8.2 Java: 11.0.6 by AdoptOpenJDK Enrichment Map version: 3.3.3.

Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHS2WXMKOCK4MUPVBHBLUDEHQPANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

Hi @veroniquevoisin thank you for your answer. I don't know how many nodes I have because when the map showed up was all gray with blue connections between nodes. Then Cytoscape stopped working. Sorry I don't understand what do you mean regarding the gmt file. I followed what they say in this protocol: Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.

Is it not correct? Thanks Rosa

[veroniquevoisin]

Hi Rosa, when you open in excel the g:Profiler table (gem format) that you have downloaded on your computer; how many rows does this table contain?

On Wed, Sep 22, 2021 at 2:49 PM rosafontana @.***> wrote:

Hi @veroniquevoisin https://github.com/veroniquevoisin thank you for your answer. I don't know how many nodes I have because when the map showed up was all gray with blue connections between nodes. Then Cytoscape stopped working. Sorry I don't understand what do you mean regarding the gmt file. I followed what they say in this protocol: Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.

Is it not correct? Thanks Rosa

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469#issuecomment-925203699, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHS373GX23M32IDBQFD3UDIQLVANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

It contains 314 rows.

[veroniquevoisin]

Try to close Cytoscape and open it again. Select Apps , EnrichmentMap and then drag and drop your gprofiler file (gem format) into the input box (see screenshot) and click on build If you can, please send a screenshot to show what's happening. [image: Screen Shot 2021-09-22 at 2.59.08 PM.png]

On Wed, Sep 22, 2021 at 2:57 PM rosafontana @.***> wrote:

It contains 314 rows.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469#issuecomment-925214848, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHSYRMSULJ57725KHA53UDIRIBANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

Sorry I can't see your screenshot. What do you mean for input? When I open the app, as you can see from my screenshot, in the data sets I open the folder that I downloaded from g:profiler. Then, as reported in the protocol, I select in the Enrichment section the txt file and in the GMT section I select the gem file (that I created by concatenating the gem for GOBP with the gem file for Reactome)

[veroniquevoisin]

Hi Rosa, just keep your first gprofiler file in the white rectangle (the gem.txt file) remove all the gmt files (hsapiens....) from the white rectangle and it should work now.\ let me know

On Wed, Sep 22, 2021 at 3:14 PM rosafontana @.***> wrote:

Sorry I can't see your screenshot. What do you mean for input? When I open the app, as you can see from my screenshot, in the data sets I open the folder that I downloaded from g:profiler. Then, as reported in the protocol, I select in the Enrichment section the txt file and in the GMT section I select the gem file (that I created by concatenating the gem for GOBP with the gem file for Reactome)

[image: Screen Shot 2021-09-22 at 12 08 50 PM] https://user-images.githubusercontent.com/90351462/134407069-b9e60903-4663-48e1-9844-9cc4d560cbc1.png

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469#issuecomment-925236577, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHS7ZKNRVMHQU2RQ3OETUDITIFANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

Hi Veronique,

Do you mean that I need to leave in the data sets section only the gem.txt file? If yes what about the concatenated gem file?

Thanks Rosa

[veroniquevoisin]

you put the concatenated .gmt file in the .gmt field (as you did) but not in the dataset section. You can try first with no gmt file , just upload the gem.txt file .

On Wed, Sep 22, 2021 at 3:25 PM rosafontana @.***> wrote:

Hi Veronique,

Do you mean that I need to leave in the data sets section only the gem.txt file? If yes what about the concatenated gem file?

Thanks Rosa

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469#issuecomment-925250479, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHSZIFCVRWLY5DWHCTBDUDIUUBANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

Hi Veronique,

thank you so much :)) Now it works. Basically, if I run the software only with the txt gem I can see the nodes but there is no label. If I run the txt together with the concatenated file I can also see the label for each node.

Thank you so much for your help

Rosa

[veroniquevoisin]

you should see the node labels in both cases: do View, Always Show graphic details to see the labels. With a gmt file , you all genes in a given pathway, with no gmt file, you only see the genes from your list: select a node and look at the heat map tab

On Wed, Sep 22, 2021 at 3:38 PM rosafontana @.***> wrote:

Hi Veronique,

thank you so much :)) Now it works. Basically, if I run the software only with the txt gem I can see the nodes but there is no label. If I run the txt together with the concatenated file I can also see the label for each node.

Thank you so much for your help

Rosa

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/469#issuecomment-925266526, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZYHSY5CYGIZOAKQ2VZPCLUDIWDDANCNFSM5EP5LDTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Veronique Voisin, PhD

Pathway and Network Analyses for OICR Cancer Stem Cell Research Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, 160 College Street, Toronto, M5S3E1. https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources https://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cells/resources http://baderlab.org/CSCPathwayAnalysisService http://baderlab.org

[rosafontana]

ohh I see! Thanks :)