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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

  1. Open Cytoscape

  2. Click on Plugins / Enrichment Map/ Load Enrichment Results

  3. Make sure the Analysis Type is set to Generic

  4. Please select the following files by clicking on the respective (...) button and selecting the file in the Dialog:
    • GMT / 'hsapiens.NAME.gmt'
    • Dataset 1 / Expression: Estrogen_expression_file.txt (OPTIONAL)

    • Dataset 1 / Enrichments: gProfiler_output_12hr.txt

    • Click on "Dataset 2 arrow_collapsed.gif" to expand the panel

    • Dataset 2 / Expression: leave empty

    • Dataset 2 / Enrichments 1: gProfiler_output_24hr.txt (OPTIONAL)

  5. Tune Parameters
    • P-value cut-off 0.01

    • Q-value cut-off 0.01

    • Check Overlap Coefficient

      • Jaccard + Overlap combined cut-off 0.5

  6. Build Enrichment Map
  7. Go to View, and activate Show Graphics Details

Step 3: Examining Results


  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.
    • NOTE: if you are using two enrichment sets you will see two different colours of edges in the enrichment map. When the set of genes in the two datasets are different (for example, when you are comparing two different species or when you are comparing results from two different platforms) the overlaps are computed for each dataset separately as there is a different set of genes that the enrichments were calculated on. In this case, since the enrichments were reduced to only a subset of most differentially expressed at each time point the set of genes the enrichments are calculated on are different and overlap are calculated for each set separately.

Software/EnrichmentMap/GProfilerTutorial (last edited 2013-06-07 03:36:58 by VeroniqueVoisin)

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