ssGSEA计算代谢Pathways Expression Le

简介

来自Identification of Metabolism-Associated Prostate Cancer Subtypes and Construction of a Prognostic Risk Model文章。作者主要使用41个代谢相关通路，用GSVA包的ssGSEA算法计算每个代谢通路在每个样本的 ssGSEA score 。

ssGSEA Assessment of Metabolism-Associated Pathways Expression Levels

Data for 41 metabolism pathway gene sets were acquired from Molecular Signatures Database (MSigDB; https://www.gsea-msigdb.org/) (10) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (11) and the PCa related activity levels were calculated using ssGSEA and the gene set variance analysis (GSVA) R package 1.34.0 (10). The metabolism-associated signatures used included galactose metabolism, ascorbate and aldarate metabolism, fatty acid metabolism, purine metabolism, pyrimidine metabolism, alanine aspartate and glutamate metabolism, glycine serine and threonine metabolism, cysteine and methionine metabolism, arginine and proline metabolism, histidine metabolism, tyrosine metabolism, phenylalanine metabolism, tryptophan metabolism, beta alanine metabolism, taurine and hypotaurine metabolism, selenoamino acid metabolism, glutathione metabolism, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, glycerolipid metabolism, inositol phosphate metabolism, glycerophospholipid metabolism, ether lipid metabolism, arachidonic acid metabolism, linoleic acid metabolism, alpha linolenic acid metabolism, sphingolipid metabolism, pyruvate_metabolism, glyoxylate and dicarboxylate metabolism, propanoate metabolism, butanoate metabolism, riboflavin metabolism, nicotinate and nicotinamide metabolism, retinol metabolism, porphyrin and chlorophyll metabolism, nitrogen metabolism, sulfur metabolism, metabolism of xenobiotics by cytochrome P450, drug metabolism cytochrome P450, and drug metabolism other enzymes ( Table S1 ).
Table S1包含着这41个通路和每个通路相关的基因。

• 第一步，准备注释文件。
  一共需要两个文件，第一是table文件，这里包含了我们自己定义的通路基因（这里是代谢通路）。