inst/shinyapp/helper/cross_gene.md

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

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

1. Expression Profile

• Normal Exp : The median gene expression in normal tissues (Including GTEx samples).
• Tumor Exp : The median 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 : The distribution of gene mutation or wild status in tumor tissues.

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

3. CNV Profile

• CNV Dist : The distribution of gene copy number variation status in tumor tissues.

• -2, homozygous deletion;

• -1, single copy deletion;
• 0, diploid normal copy;
• 1: low-level copy number amplification;

• 2: high-level copy number amplification

• CNV Amp : The percentage of gene copy number amplification (1,2) in tumor tissues.

• CNV Del : The percentage of gene copy number deletion (-1, -2) in tumor tissues.

4. Transcript Profile

• Selected transcript(s) of one gene : The median transcript expression in tumor tissues.

5. Methylation Profile

• Selected CpG sites of one gene : The median beta value of CpG sites 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
• Transcript: TcgaTargetGtex_rsem_isoform_tpm
• Methylation: GDC-PANCAN.methylation450.tsv

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