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mskspi / PathCNN

Interpretable convolutional neural networks on multi-omics data predict long-term survival in glioblastoma
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Question about pathway in KEGG #4

Closed Y-Claw closed 1 year ago

Y-Claw commented 1 year ago

Hi, When I tried to replicate your experiment from scratch, I found some pathways that were not found in the KEGG hsa pathway, such as SELENOAMINO_ACID_METABOLISM and DORSO_VENTRAL_AXIS_FORMATION. VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS contains only 4 genes in the hsa pathway, which cannot be processed into 5-dimensional data using PCA. Could you please provide more details about pathway and the genes used in pathway?

mskspi commented 1 year ago

Hi, We used only 146 KEGG pathways that are available in the 'data' folder, removing disease-specific pathways. For associated genes for each pathway, the c2.cp.kegg.v5.2.symbols.gmt was used, which was downloaded from the gsea-msigdb database.

Y-Claw commented 1 year ago

Get it, thank you very much.