Characterization of Immune Gene Signatures among the SKCM Immune clusters
This protocol is extracted from research article:
Decoding Immune Heterogeneity of Melanoma and identifying immune-prognostic hub genes
J Cancer, Jan 1, 2021; DOI: 10.7150/jca.50277

Cytolytic activity (CYT) was computed using an already validated gene expression signature using the geometric average of granzyme A (GZMA) and perforin-1 (PRF1) gene expression 17. Tumor Inflammation Signature (TIS) was quantified using the average of continuous mean of log2-transformed normalized expression of known genes 18. Relative antigen presentation machinery (APM) was quantified using a validated gene expression signature 19. Pathological assessment of the proportion of tumor infiltrating lymphocytes (TILs) 20 was also used.

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