Fig. 6
Proteomic pathway ORA results and comparison of the transcriptomic and proteomic data sets. (a) Top 20 pathways found enriched by ORA in the cellular proteome, filtered for cancer-related pathways and sorted according to the smallest padj value. (b) Cancer-related pathways found enriched by ORA in the EV proteome, sorted according to the smallest padj value. a + b. The y-axis shows the respective database as well as the name of the pathway. The circle diameter shows the number of proteins participating in the pathway that were found differentially expressed in the proteomics data. Colors and symbols indicate the treatment in which the pathway was found to be significantly enriched compared to the DMSO control. GO BP = Gene Ontology Biological Process; GO MF = Gene Ontology Molecular Function; MSigDB: Molecular Signatures Database; KEGG: Kyoto Encyclopedia of Genes and Genomes42,43,44. (c) UpSet plot of the genes found differentially expressed on both cellular transcriptomic and proteomic levels. The gene names found differentially expressed in at least four different treatment-analysis combinations were added to the plot. Underlined genes are part of the final biomarker signature proposed below.
