Comprehensive Analysis of Tumor Immune Infiltrates

TIMER is a comprehensive resource for systematic analysis of immune infiltrates across diverse cancer types (https://cistrome.shinyapps.io/timer/) (23 (link)). TIMER applies a deconvolution previously published statistical method (24 (link)) to infer the abundance of tumor-infiltrating immune cells (TIICs) from gene expression profiles. The TIMER database includes 10,897 samples across 32 cancer types from The Cancer Genome Atlas (TCGA) to estimate the abundance of immune infiltrates. We analyzed LAYN expression in different types of cancer and the correlation of LAYN expression with the abundance of immune infiltrates, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, via gene modules. Gene expression levels against tumor purity is displayed on the left-most panel (25 (link)). In addition, correlations between LAYN expression and gene markers of tumor-infiltrating immune cells were explored via correlation modules. The gene markers of tumor-infiltrating immune cells included markers of CD8+ T cells, T cells (general), B cells, monocytes, TAMs, M1 macrophages, M2 macrophages, neutrophils, natural killer (NK) cells, dendritic cells (DCs), T-helper 1 (Th1) cells, T-helper 2 (Th2) cells, follicular helper T (Tfh) cells, T-helper 17 (Th17) cells, Tregs, and exhausted T cells. These gene markers are referenced in prior studies (26 (link)–28 (link)). The correlation module generated the expression scatter plots between a pair of user-defined genes in a given cancer type, together with the Spearman's correlation and the estimated statistical significance. LAYN was used for the x-axis with gene symbols, and related marker genes are represented on the y-axis as gene symbols. The gene expression level was displayed with log2 RSEM.