Basic information

Phenotype

xcell: microenvironment score

Description

Score representing the proportion of microenvironment in a tumor sample. Calculated as the sum of the xCell Immune and Stroma scores. The scores were inferred using RNA data.

Source

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1349-1

Method

The R package immunedeconv (V2.0.4) (PMID: 31510660) was used to perform immune cell deconvolution using RNA expression data (TPM).

Gene association

Number of significant genes with P-value ≤ 10^-6 for each cohorts are summarized in bar plots. The scatter plot highlights significant associations diven by protein rather than mRNA abundance.

Association of protein abundance of genes

Protein RNA SCNV

		Signed p-values
Gene	Meta P	BRCA	CCRCC	COAD	GBM	HNSCC	LSCC	LUAD	OV	PDAC	UCEC

* P-values for individual cohorts can be clicked to show the data plots. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with xcell: microenvironment score to WebGestalt.

Phosphosite association

Number of significant genes with P-value ≤ 10^-6 for each cohorts are summarized in the bar plot. The scatter plot highlights significant associations diven by phosphorylation rather than protein abundance.

* P-values for individual cohorts can be clicked to show the data plots.

Gene set enrichment analysis

Submit phosphorylation sites and the common logarithm of the p-values of their association with xcell: microenvironment score to WebGestalt.