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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
  1. T: describes the size of the original (primary) tumor and whether it has invaded nearby tissue
  2. N: describes nearby (regional) lymph nodes that are involved
  3. M: describes distant metastasis (spread of cancer from one part of the body to another)
  4. Stage: describes the progression of cancer
  5. Grade: describes the differentiated level of cancer
  6. low-advanced cancers: early-stage (Stage I-II) or low-grade (Grade I-II) cancers
  7. highly-advanced cancers: late-stage (Stage III-IV) or high-grade (Grade III-IV) cancers
  8. tumor mutation burden: the total number of substitutions, regardless of somatic mutation type in tumor