inst/shinyapp/helper/cross_pw.md

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

Visualize multi-omics profile of one pathway among TCGA cancer types

1. Expression Profile

• Normal ssGSEA : The median ssGSEA  gene expression in normal tissues (Including GTEx samples).
• Tumor ssGSEA : The median ssGSEA  gene expression in tumor tissues.
• T vs. N(Wilcox) : The Wilcoxon test between tumor and normal samples (P<0.001, "***"; P<0.01, "**"; P<0.05, "*"; P>0.05, "-").

Bar plot: The 0~1 normalization on TPM expression data.

2. Mutation Profile

• Mutation Dist Mean: The distribution of mutation or wild pathway gene status in tumor tissues. If one of pathway genes is mutated, it is considered as mutation. 

• Mutation PCT Mean: The percentage of pathway mutation status in tumor tissues.

• Mut.Genes Mean: The mean counts of mutated pathway genes in tumor tissues.

3. CNV Profile

• CNV Dist Mean: The distribution of pathway gene copy number variation status in tumor tissues.
• Amp, homozygous deletion or single copy deletion;
• Non, diploid normal copy;

• Del, Copy number amplification.

• Amp.Genes Mean : The copy number amplification percentage of pathway genes  in tumor tissues.

• Del.Genes Mean : The copy number deletion percentage of pathway gene in tumor tissues.

Data source—

• mRNA: TcgaTargetGtex_rsem_gene_tpm
• Mutation: mc3.v0.2.8.PUBLIC.nonsilentGene.xena
• CNV: TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes

UCSCXenaShiny documentation built on Aug. 8, 2025, 7:19 p.m.