Closed sarneg closed 6 months ago
If I understand your issue correctly, instead of using the rnk file from the Edb directory for your expression file you can use your original file that you uploaded to run your analysis with GSEA.
The only issue that I think you will have is that you have given GSEA an expression file ensembl id and gene name and I think GSEA is translating those for you into and rank file with just gene name
Are you creating your enrichment directly from within the GSEA interface or are you using the EM input panel inside cytoscape?
Thanks, Ruth
I am using enrichment directly within GSEA and uploading original expression file after swapping gene name and ensemble id worked. Now I have heatmaps with gene expression for each sample. Thank You.
My other queries
I want to make heatmaps of different nodes after filtering genes based on fold change and p-values.
I also want to make a Network map of few selected nodes with each node showing their String network for proteins.
I would like to highlight my protein of interest (that was silenced using siRNA) in this Network.
I am using enrichment directly within GSEA and uploading original expression file after swapping gene name and ensemble id worked. Now I have heatmaps with gene expression for each sample. Thank You.
My other queries
I want to make separate heatmaps of a few nodes after filtering genes based on fold change and p-values.
I also want to make a Network map with few selected nodes with each node showing their String network for proteins.
I would like to highlight my protein of interest (that was silenced using siRNA) in this Network.
Thank you in advance
On Thu, 18 Jan 2024 at 17:20, Ruth Isserlin @.***> wrote:
If I understand your issue correctly, instead of using the rnk file from the Edb directory for your expression file you can use your original file that you uploaded to run your analysis with GSEA.
The only issue that I think you will have is that you have given GSEA an expression file ensembl id and gene name and I think GSEA is translating those for you into and rank file with just gene name rank. If you want to keep all of your results as is, you can create a separate expression file from your original expression and swap your ensembl id column and your gene name column and use that instead of the rank file for the expression file.
Are you creating your enrichment directly from within the GSEA interface or are you using the EM input panel inside cytoscape?
Thanks, Ruth
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The are a few different ways to highlight your gene of interest in the network.
I am doing GSEA analysis on desktop application. I have two RNAseq experiments.
I have 3 replicates for each condition. My goal is to do pathway analysis for both treatments (siRNA and drug) and to see how similar/different the two treatments are. Note: My controls from both experiments are different as control treatments may have different effects on gene expression. I run separate GSEA for the two experiments.
I have expression data of all samples from both experiments. I am using Ensembl id for column "Name" and Gene names for column "Description". I choose desired phenotype label and run GSEA for each experiment separately.
Then I run enrichment map visualization. I select result of desired experiment to visualize enrichment Map. It selects GSEA analysis for dataset 1. It selects rnk from edb folder for expression. Then on cytoscape, I get my networks. I get heatmaps for nodes with the ranking of genes. I need the heatmap with expression values in each sample and want to filter genes based on fold change and p-values.
I also want to make a Network map of few selected nodes with each node showing their String network for proteins.
I would like to highlight my protein of interest (that was silenced using siRNA) in this Network.