Quantifying Immune Signatures in Tumors

For a pathway, immune signature, or biological process, we quantified its enrichment level in a tumor sample as the single-sample gene-set enrichment analysis (ssGSEA) (52 (link)) score of its marker genes. The marker gene sets representing different immune signatures were from several publications, including CD8+ T cells (36 (link)), CD4+ regulatory T cells (36 (link)), pro-/anti-inflammatory cytokines (36 (link)), and M1/M2 macrophages immune cytolytic activity (36 (link)), and proliferation signature score (53 (link)). These gene sets are listed in Supplementary Table S4.

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Li M., Gao X, & Wang X. (2023). Identification of tumor mutation burden-associated molecular and clinical features in cancer by analyzing multi-omics data. Frontiers in Immunology, 14, 1090838.

Publication 2023

Anti inflammatory Biological process Cd8 t cells Cytokines Gene Genes marker Macrophages Regulatory t cells Tumor

Corresponding Organization : China Pharmaceutical University

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Variable analysis

independent variables

SsGSEA score of marker genes for different immune signatures

dependent variables

Enrichment level of different pathways, immune signatures, or biological processes in a tumor sample

control variables

The marker gene sets representing different immune signatures from several publications, including CD8+ T cells, CD4+ regulatory T cells, pro-/anti-inflammatory cytokines, M1/M2 macrophages immune cytolytic activity, and proliferation signature score

controls

No positive or negative controls were explicitly mentioned in the input.

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