Fig. 5: Transcriptomic profiling reveals tumor antigen gene expression and immune composition.
From: Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics
a Principal component analysis of bulk RNA sequencing data sets. Supervised heatmap using HLA peptide (b) and protein (c) information as input. Protein symbols were converted to gene symbols to match the gene symbols in the transcriptomics data. Transcript abundance (normalized) is indicated in the heatmap using the blue-red scale (blue for low and red for high abundance). Metadata if the samples (subgroup and sex) can be distinguished using different colors. Furthermore, the significance column indicates whether a gene symbol was found during the differentially expression analysis of the transcriptomics data in subgroup comparisons (see Supplementary Fig. 9). Relative frequencies of lymphocytes and myeloid cells (d), as well as a dedicated lymphoid (e) and myeloid (f) panel, are based on deconvolution of transcriptomics data. The deconvolution is performed with published data, which shows an accurate observation of the identified cell types in the dataset99,100. Source data are provided as a Source Data file.
