Table 1 A summary of TCOA functions and data display
From: The Cancer Omics Atlas: an integrative resource for cancer omics annotations
Module | Function | Visualization |
|---|---|---|
Gene | show mean gene expression values in different cancer types | bar chart |
compare gene expression between cancer and normal samples | box plot | |
show expression correlation between gene and gene in cancers | scatter diagram | |
compare gene expression between different cancer phenotypes (T, N, M, Stage and Grade) | box plot | |
compare survival time between gene higher-expression-level and lower-expression-level cancers | survival curve | |
show gene somatic mutation rates in cancers | bar chart | |
compare gene somatic mutation rates between different cancer phenotypes (T, N, M, Stage and Grade) | box plot | |
classify gene somatic mutations in cancers | pie chart | |
compare survival time between gene-mutated and gene-wildtype cancers | survival curve | |
compare gene expression between gene-mutated and gene-wildtype cancers | box plot | |
MicroRNA | show mean miRNA expression values in different cancer types | bar chart |
compare miRNA expression between cancer and normal samples | box plot | |
show expression correlation between gene and miRNA in cancers | scatter diagram | |
show expression correlation between miRNA and miRNA in cancers | scatter diagram | |
compare miRNA expression between different phenotypes (T, N, M, Stage and Grade) in cancers | box plot | |
compare survival time between miRNA higher-expression-level and lower-expression-level cancers | survival curve | |
Cancer | show mutation rates of the 50 most frequently mutated genes in the cancer type | bar chart |
show the up-regulated and down-regulated genes in the cancer type satisfying the threshold given by users | bar chart | |
show important pathways associated with the highly-expressed genes in the cancer type | bar chart | |
show the up-regulated and down-regulated miRNAs in the cancer type satisfying the threshold given by users | bar chart | |
Pan-cancer | show pathways significantly up-regulated in cancers | bar chart |
show genes whose upregulation is associated with poor prognosis in cancers | survival curve | |
show genes whose downregulation is associated with poor prognosis in cancers | survival curve | |
show genes with increased or decreased expression alterations consistently from normal tissue to low-advanced cancers, and from low-advanced cancers to highly-advanced cancers | bar chart | |
show the cell cycle pathway consistently up-regulated in cancers | bar chart | |
show genes whose expression levels are significantly higher or lower in cancers than in normal tissue | table | |
show genes whose expression levels are significantly higher or lower in high-grade cancers than in low-grade cancers | table | |
show genes whose expression levels are significantly higher or lower in late-stage cancers than in early-stage cancers | table | |
compare tumor mutation burden among different cancer types | bar chart | |
Immuno-Oncology | query molecular profiles of 2877 immune-related genes in cancers | the same as the “Gene” module |
Protein | show mean protein expression levels (normalized) in different cancer types | bar chart |
show expression correlation between gene and protein in cancers | scatter diagram | |
compare protein expression between different cancer phenotypes (T, N, M, Stage and Grade) | bar chart | |
compare survival time between protein higher-expression-level and lower-expression-level cancers | survival curve |