Merge Tool to visualise communalities between two networks

[LilliThePink]

Dear GitHub Community, can anyone help me with the following problem, please?

We treated two different cell lines with our substance of interest (in triplicates) and had RNA sequencing analysis done on the treated cells and controls.
The sequencing results were analysed, aligned and read counts generated by the core facility. They used the CLC software (based on EdgeR) to create pre-ranked lists. Based on these pre-ranked lists, I conducted Gene Set Enrichment Analysis (GSEA preranked). Results showed that, with a cut-off FDR of 0.25, cell line 1 had 124 gene sets down-regulated by the treatment, none up-regulated, cell line 2 had 1397 down-regulated gene sets, 145 up-regulated.
Out of all regulated gene sets, 66 down-regulated gene sets appear in both cell lines, i.e. they are the common gene sets regulated in both cell lines. Now I want to visualise and annotate these 66 result using CytoScape.

Hence, I went on to create two separate networks of the gene sets regulated by the treatment using Enrichment Map, one for cell line 1 and one for cell line 2. I did so by using the GSEA results folders and GMT-files as input and applied a cut-off of FDR 0.25. Since we are most interested in the 66 regulated gene sets that both cell lines have in common, I tried to use the Merge Networks tool and selected intersection. But no matter how I chose the settings (merge nodes only and ignore edges or enable merging nodes/edges in the same network), the merged network shows up with 124 nodes (the same number as in cell line 1's network) instead of 66 only. What am I doing wrong?
THANK YOU for helping!! Lilli

[risserlin]

Have you tried creating one enrichment map with both of your datasets?
Once you create a network with both of the datasets you can colour your network by dataset and clearly highlight the nodes that are found in both datasets.

[LilliThePink]

Dear Ruth, so sorry for the late reply. I got sidetracked by another project. Your recommendation is certainly very helpful and I am currently re-visiting my Cytoscape network trying to visualise what I need. THANK YOU so much for your help!!! Lilli

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________________________________ Von: Ruth Isserlin ***@***.***> Gesendet: Dienstag, 17. September 2024 14:51 An: BaderLab/EnrichmentMapApp ***@***.***> Cc: Lilli Brandtner ***@***.***>; Author ***@***.***> Betreff: Re: [BaderLab/EnrichmentMapApp] Merge Tool to visualise communalities between two networks (Issue #551) Have you tried creating one enrichment map with both of your datasets? Once you create a network with both of the datasets you can colour your network by dataset and clearly highlight the nodes that are found in both datasets. — Reply to this email directly, view it on GitHub<#551 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BLLH4QVQP42O2CGZ3BPGPATZXAQUTAVCNFSM6AAAAABOLBCMROVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJVGY3TGOBSHA>. You are receiving this because you authored the thread.Message ID: ***@***.***>