The short guidance for visualization of gene set enrichment analysis (GSEA) or gene set overrepresentation analysis (Enrichr, DAVID, Great, BiNGO) results using Cytoscape. Presented as a part of the Gene Set Analysis and Visualization Workshop, October 2017, University of Manitoba, Winnipeg, Canada.

1. Gene Set Analysis and
Visualization Workshop
Part II: Visualization
Svetlana Frenkel, PhD

2. Visualization of the gene set
analysis results
Enrichment Map
Cytoscape can read network/pathway files
written in the following formats:
Simple interaction file (SIF or .sif format)
Nested network format (NNF or .nnf format)
Graph Markup Language (GML or .gml format)
XGMML (extensible graph markup and modelling
language)
SBML
BioPAX
PSI-MI Level 1 and 2.5
GraphML
Delimited text
Excel Workbook (.xls, .xlsx)
Cytoscape.js JSON 2

3. GSEA result example
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4. Transfer the GSEA result to Cytoscape
Cytoscape has to be installed and launched!
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5. GSEA result in the Cytoscape default
style
Control
panel
Table
panel
Results
panel
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6. Step 1: change labels
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7. Step 2: Change scale and rotate
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8. Step 3.1: Change node
presentation parameters
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9. Step 3.2: Change edges
presentation parameters
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10. Step 4: Change node size
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11. Step 5: Node groups
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12. Step 6: Change or remove label
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13. Step 7: Create text annotation
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14. Result
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15. Change the network style
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16. Step 8: change edges width
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17. Step 9: set the custom edge colors
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18. Final result
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19. Image exporting options
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20. Visualization of Enrichr result
Cytoscape options for creating networks:
• Import fixed-format network files
• Import networks from unformatted table files
Enrichment Map plugin options:
• Create network from GSEA result
• Create network from generic or gProfiler result
• Create network from DAVID, BinGO or Great
result
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21. Category Term Count % PValue Genes
List
Total
Pop
Hits
Pop
Total
Fold
Enrichme
nt
Bonferron
i Benjamini FDR
GOTERM_
BP_DIRECT
GO:0060070~can
onical Wnt
signaling pathway 12 0.21 3.21E-17
WNT2, NDP, LRP6, LEF1,
HOXB9, LRRK2, MYC,
AXIN1, CTNNB1, LRP5,
APC, DVL1 40 83 16792 60.69 3.25E-14 3.25E-14 5.08E-14
GOTERM_
CC_DIRECT
GO:1990909~Wnt
signalosome 7 0.12 2.94E-14
WNT2, LRP6, LRRK2,
CTNNB1, LRP5, APC, DVL1 40 11 18224 289.92 4.32E-12 4.32E-12 3.50E-11
Term Overlap P-value
Adjusted
P-value
Old P-value
Old Adjusted
P-value
Z-score
Combined
Score
Genes
canonical Wnt signaling
pathway involved in
negative regulation of
apoptotic process
24/371 6.27E-32 1.88E-28 4.61E-27 1.38E-23 -5.11 367.33
LRRK2;LEF1;AXIN1;LRP5;HMGA2;CIB1;H
SPD1;LRP6;ZNF16;HCK;HOXB9;IRAK1;UB
B;APC;TRAF6;MYC;DVL1;UBC;BCL2;CD27
;CTNNB1;NDP;WNT2;UBA52
canonical Wnt signaling
pathway involved in
positive regulation of
apoptotic process
21/279 5.26E-29 7.88E-26 1.18E-24 1.78E-21 -4.35 283.64
LRRK2;LEF1;DAB2IP;AXIN1;LRP5;HMGA2
;TNF;HSPD1;LRP6;HOXB9;UBB;APC;TRAF
6;MYC;DVL1;UBC;CTNNB1;NDP;HRG;WN
T2;UBA52
Visualization of Enrichr resultDAVIDEnrichr
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22. Visualization of Enrichr/DAVID
result 1
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23. Visualization of Enrichr/DAVID
result 2
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24. Visualization of Enrichr/DAVID
result 3
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25. Visualization of Enrichr/DAVID
result 4
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26. Visualization of Enrichr/DAVID
result 5
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27. Enrichr result in the default style
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28. Change node label, color and size
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29. Select nodes from the table
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30. Custom styles for node groups and genes
Signaling pathways
Other functions
CDC20 activity
DefensinsLigand-
binding
Custom styles for nodes:
• Diamond glyph – MAPK signaling
• Triangle glyph – FGFR signaling
• Red border – Apoptosis and/or TP53 activity
Custom styles for edges:
• Teal + Transparency=200 for all edges contain NFKB2
• Pink + Transparency=200 for all edges contain AXIN1
(Transparency=30 for all other edges) 30

31. Enrichr results example
• Enrichr output using four gene set libraries:
GO biological process, GO molecular
function, KEGG, Reactome
• Removed all gene sets larger than 700 and
smaller than 10 genes
• 2083 pathways
• 1939 significant with q-value<0.1
• 1823 significant with q-value<0.05
• 1335 significant with q-value <0.01
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32. Enrichr results example:
1939 significant with q-value<0.1
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Style tuning: node
labels are removed,
node shape is linked to
the gene set description
(i.e. library)

33. Enrichr results example:
1335 significant with q-value <0.01
Node size is linked to
the number of
overlapped genes in
gene set
Node color is linked
to the q-value
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34. Enrichr results example:
1335 significant with q-value <0.01
Custom edge color
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35. Layouts
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36. Layout examples
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