Table 1.
Current Firehose data content (Some of these data may not be accessible due to TCGA data restrictions, full data table can be accessible via http://gdac.broadinstitute.org/runs/stddata__2014_03_16/ingested_data.html).
Figure 1.
Overall RTCGAToolbox structure and workflow.
(A) Overall representation of RTCGAToolbox layers from Firehose web portal to user environments. (B) Sample workflow for “BRCA” dataset.
Table 2.
Data types supported by RTCGAToolbox.
Figure 2.
Sample heatmap outputs from BRCA dataset.
Panel A and B show the top differentially up and down regulated genes between “Cancer” and “Normal” samples by using RNASeq and microarray data respectively.
Figure 3.
A KM plot that compares the survival difference between PIK3CA, which is the gene has highest mutation frequency in BRCA dataset, high and low expressed samples.
Figure 4.
Summary plot for BRCA dataset.
A circle plot that shows the differentially expressed genes result from RNASeq and microarray platform (Inner circle 1 and 2, y axis represents the fold change value, red dots are up regulated and blue dots are down regulated in cancer samples), copy number changes (inner third circle, blue zones represents the deletions and red circle represents the amplifications) and outer circle shows the genes that has mutation at least 5% of samples.