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Gene expression data

YT Yi-Ching Tang
AG Assaf Gottlieb
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Gene expression data were measured by transcripts per million (TPM) and log-transformed. We imputed with mean for the rest of missing values. Enrichment score (ES) of each PID pathway in each cell line was calculated using the single-sample Gene Set Enrichment (ssGSEA) algorithm52 through GSEApy (https://gseapy.readthedocs.io/en/master/gseapy_example.html). We ran permutation test for 1000 times and normalized ES scores by the size of gene set to obtain normalized ES (i.e., NES). We used the resulting pathway enrichment matrix with size of 319 cancer cell lines by 196 pathways as the gene expression feature (EXP).

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