DriverDBv3: A database for human cancer driver gene research



Summary network

The Gene Summary provides a visualization of different features of a user-selected gene in relation with multiple cancer types.


  • The Differential expression (DE) squares indicate whether a gene is significant with p value <0.05 and whether it is differentially expressed. Red represents up-regulated genes with log2(fold change) > 1 and green represents down-regulated genes with log2(fold change) < -1.
  • The Mutation squares indicate the number of mutation tools which identify this gene as a mutation driver. As the number of tools goes from low to high, the blue color goes from light to deep, correspondingly.
  • The Copy Number Variation (CNV) squares indicate CNV gain or loss of a gene. Red represents a gain (1) and green represents a loss (-1).
  • The Methylation squares indicate whether the gene is hyper-methylated (1) or hypo- methylated (-1). Red represents hyper and green represents hypo.
  • The Survival squares indicate whether this is survival-relevant with log-rank p value < 0.05. Red represents oncogene with log2(hazard ratio) > 0 and green represents tumor suppressor gene with log2(hazard ratio) < 0.
  • The miRNA squares indicate the number of miRNAs that interacts with this gene. As the number of miRNA goes from low to high, the orange color goes from light to deep, correspondingly.

The Gene Expression function provides visualizations to illustrate the expression of a user-selected gene across multiple cancer types.


Visualization of all cancer types

The boxplots show the distribution of expression of all cancer types for a user-selected gene. The expression are grouped in 2 ways: by sample type and by mutation class.

By sample type

By mutation class


Visualization of each cancer type

Grouping By


Cancer Type

Visualization

The Gene Mutation function provides visualizations to illustrate mutation statistics in correspondence to protein regions and exons in multiple cancer types.



Visualization of all cancer types


Visualization of each cancer type

Visualization By


Cancer Type

Visualization


The Gene CNV function provides visualizations to illustrate the copy number gain or loss of a user-selected gene across multiple cancer types.


Copy number variation in all cancer

This graph shows the copy number variation (CNV) of a user-selected gene in several cancer types. Each gene is analyzed by two CNV tools: iGC and diggit. The sample proportion is shown in the plot when the cancer is identified by one or both of the tools.


Visualization of each cancer type

Cancer Type

Visualization


CNV Table

The Gene Methylation function provides visualizations to illustrate the methylation type of a user-selected gene across multiple cancer types.


Copy number variation in all cancer

This graph shows the methylation type of a user-selected gene in several cancer types. Each gene is defined by two methylation tools: methylmix and ELMER. The sample proportion is shown in the plot only when the cancer is identified by both tools.


Visualization of each cancer type

Cancer Type

Visualization


Methylation Table

The Gene Survival function provides visualizations to illustrate the survival probability of a user-selected gene across multiple cancer types.


Single Gene Survival

This table provides detailed survival information of a single gene and also serves as a control panel to produce the Kaplan-Meier plot below.

Survival Table


Kaplan-Meier plot


Survival Network

The Gene Survival network illustrates the synergistic effect of a user-selected gene and its related genes. The synergistic effect is defined by the HR of the user-selected gene and its related genes. If the HR of two genes is greater than 1.5 folds of each, these two genes are identified to have a synergistic effect, and are further divided into 2 levels – 1.5 folds and 2 folds; each with a positive and negative direction of HR.

Survival of synergistic effect

This section provides all gene pairs (a user-selected genes and its related genes) with HR fold change greater than each single gene in both directions even though only more than 1.5 fold changes are considered to have a synergistic effect between them. For each gene pair, the patients are stratified to two groups based on their expression median. The groups of patients are then compared on their 5-year overall survival (OS) probability over months, as shown in the plots.

The Gene miRNA function provides visualizations to illustrate the relations between a user-selected genes and miRNAs across multiple cancer types.


miRNA-gene network

The Gene miRNA network illustrates the relations between a user-selected gene and miRNAs. The interactions are defined by 12 prediction tools or experimental validations recorded by miRTarBase. Validated relations are represented by solid lines; predicted relations are represented by dotted lines. Predicted relations can be further filtered by a minimum of 6, 8, or 10 tools.


Gene-miRNA table



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