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Enrichment Map g:Profiler Tutorial


This quick tutorial will guide you through the generation of an Enrichment Map for an analysis performed using g:Profiler (Functional Profiling of Gene List from large-scale experiments)

To run this tutorial:

Description of the tutorial files contained in the gProfilerTutorial folder:


Step 1: Generate g:Profiler output files

  1. Go to g:Profiler website - http://biit.cs.ut.ee/gprofiler/

  2. Select and copy all genes in the tutorial file 12hr_topgenes.txt in the Query box

  3. In Options, check Significant only, No electronic GO annotations

  4. Set the Output type to Generic EnrichmentMap

  5. Show advanced options

  6. Set Max size of functional category to 500

  7. Set Significance threshold to Benjamini-Hochberg FDR

  8. Click on g:Profile! to run the analysis

  9. Download g:Profiler data as gmt: name

  10. Download the result file: Download data in Generic Enrichment Map (GEM) format

Note: repeat these steps for the 24hrs time-point and the file 24hr_topgenes.txt


Screenshot gProfilet EM Panel

Step 2: Generate Enrichment Map with g:Profiler Output

Step 3: Examining Results

gProfiler EM Result

  1. Node (inner circle) size corresponds to the number of genes in dataset 1 within the geneset
  2. Node border (outer circle) size corresponds to the number of genes in dataset 2 within the geneset
  3. Colour of the node (inner circle) and border(outer circle) corresponds to the significance of the geneset for dataset 1 and dataset 2, respectively.
  4. Edge size corresponds to the number of genes that overlap between the two connected genesets. Green edges correspond to both datasets when it is the only colour edge. When there are two different edge colours, green corresponds to dataset 1 and blue corresponds to dataset 2.

Software/EnrichmentMap/GProfilerTutorial (last edited 2015-05-29 14:28:54 by VeroniqueVoisin)

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