Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions
Fig 3
The t-SNE plot of 64-dimensional latent features of all samples in the METABRIC and TCGA BRCA dataset and the Kaplan-Meier survival curve of and 415 TCGA BRCA luminal-A breast cancer samples.
(A) The t-SNE plot of all samples in the METABRIC and TCGA BRCA datasets. The samples of METABRIC and TCGA BRCA are denoted as circle and square, respectively. The samples assigned to the BPS-LumA and WPS-LumA colored as green and orange, respectively. (B) The Kaplan-Meier survival curve of the 415 TCGA samples which were assigned to the closer prognostic subgroups (BPS-LumA and WPS-LumA) in the latent space. (C) The mean log2-transforemd expression levels and (D) the log-transformed median absolute deviation of individual genes (N = 17,202) in the METABRIC (microarray, x-axis) and the TCGA (RNA-seq, y-axis) dataset were plotted using scatter plots. Each dot indicates individual genes in the (C) and (D).