How to use output of PANTHER Enrichment Test as input to cytoscape

Question

[kousi31]

PANTHER Enrichment Test gives output as tabular format. How to get output as xml format or is there a way to import panther output into cytoscape?

Please help, I am learning pathway analysis and new to cytoscape.

[Kevin Blighe]

Hello. Your post is lacking in details, so, it will likely not receive any answer. Which PANTHER resource are you using?; Have you read the Cytoscape documentation in order to understand which input format(s) is / are required?; Have you searched [via your search engine of choice] for keywords panther export cytoscape?

[kousi31]

I tried http://www.pantherdb.org/ --> Statistical enrichment test.
Export options for result are Table XML with user input ids JSON with user input ids

Output table

PANTHER Pathways number overUnder pvalue fdr
Wnt signaling pathway (P00057) 268 + 0.00E00 0.00E00
Cadherin signaling pathway (P00012) 133 + 0.00E00 0.00E00
Integrin signalling pathway (P00034) 176 + 7.36E-14 3.90E-12
Alzheimer disease-presenilin pathway (P00004) 103 + 1.71E-13 6.78E-1

Input formats supported by cytoscape does not look this.
The gml output format given by gprofiler look like this.
This is easily imported into EnrichmentMap

GO.ID Description p.Val FDR Phenotype Genes
GO:0048015 phosphatidylinositol-mediated signaling 5.63e-16 5.63e-16 1 HGF,FGFR2,FGFR3,PIK3CG,GATA3,PIK3CA,FLT3,SOX9,PDGFRA,TP53,AKT1,PIK3R1,EGFR,KIT,PTEN,ERBB4,NF1,MTOR
GO:0048017 inositol lipid-mediate signaling 6.25e-16 6.25e-16 1 HGF,FGFR2,FGFR3,PIK3CG,GATA3,PIK3CA,FLT3,SOX9,PDGFRA,TP53,AKT1,PIK3R1,EGFR,KIT,PTEN,ERBB4,NF1,MTOR
GO:0048732 gland development 6.48e-16 6.48e-16 1 HGF,FGFR2,GATA3,FBXW7,SOX9,TBX3,BRCA2,AKT1,ARID5B,ARHGAP35,ELF3,AR,ERBB4,WT1,NF1,CEBPA

I am working in chicken RNA-seq data set. I tried the protocol as given this paper. I want to use GSEA. But GSEA Msigdb has human pathways.
I want to know if panther output can be downloaded as gml format?
Or Is there a way to download panther pathways in GMT format which I can use in GSEA? I have just started learning pathway analysis. Kindly help.

[Kevin Blighe]

It implies that XML output format is available (?)

The GMT format is easy to construct manually: A: Running GSEA for DEGs