HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Phenotype
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION
Description
Enrichment score representing genes involved in the epithelial to mesenchymal transition. The score was calculated using ssGSEA on the RNA data (Z-score transformed coding genes with expression in at least 50% of the samples in a cohort).
Source
http://www.gsea-msigdb.org/gsea/msigdb/cards/HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.html
Method
Single sample gene set enrichment analysis (ssGSEA) was performed for each cancer type using gene-wise Z-scores of the RNA expression data (RSEM) for the MSigDB Hallmark gene sets v7.0 (PMID: 26771021) via the ssGSEA2.0 R package (PMID: 30563849). RNA data were filtered to coding genes with < 50% 0 expression. (Parameters: sample.norm.type="rank", weight=0.75, statistic="area.under.RES", nperm=1000, min.overlap=10). Pathway activity scores are normalized enrichment scores from ssGSEA.
Genes
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

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 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 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.

Signed p-values
Gene Protein Site 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.

Gene set enrichment analysis

Submit phosphorylation sites and the common logarithm of the p-values of their association with HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION to WebGestalt.