veroniquevoisin
commented
2 years ago Hi Rosa, This github issue tracker was designed to report bugs and enhancement ideas regarding the Cytoscape EnrichmentMap app. To quickly respond to your questions, the expression file is optional, you can leave the field empty. The format to create the expression file is described in the protocol. You can construct it with any values that you find interesting and relevant for your project, these values will be displayed in the heatmap tab when you click on a node of interest. It could be the normalized intensity values of your proteomics data if suited. The g:Profiler recommendation in the Nature Protocol is good for any defined gene list, RNAseq, proteomics or other omics-data. Thanks, veronique
On Mon, Sep 27, 2021 at 3:21 PM rosafontana @.***> wrote:
Hi,
I'm following your Nature protocol Reimand et al., 2019 to analyze my mass spec data and it's really helpful :) I would like to ask you which data are required to generate the expression file to run on Enrichment Map when you are working with mass spec data. Since I am new to doing this kind of analysis, I would like to ask you if there are specific advice that I need to follow in order to analyze proteomic data when I use g: Profiler and Enrichment Map. For example, are there some settings specifically different between RNAseq and proteomic data analysis with g: Profiler and Enrichment Map? Moreover, before submitting the list on g:Profiler how do you recommended ranking it? Based on p-value or fold increase over control expression?
Thanks
Rosa
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-- 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,
I'm following your Nature protocol Reimand et al., 2019 to analyze my mass spec data and it's really helpful :) I would like to ask you which data are required to generate the expression file to run on Enrichment Map when you are working with mass spec data. Since I am new to doing this kind of analysis, I would like to ask you if there are specific advice that I need to follow in order to analyze proteomic data when I use g: Profiler and Enrichment Map. For example, are there some settings specifically different between RNAseq and proteomic data analysis with g: Profiler and Enrichment Map? Moreover, before submitting the list on g:Profiler how do you recommended ranking it? Based on p-value or fold increase over control expression?
Thanks
Rosa