Total RNA was extracted from formalin-fixed, paraffin-embedded tissue samples using the HighPure RNA Extraction Kit (Roche Applied Science, Indianapolis, IN) and subjected to gene expression profiling (GEP) as described previously (5 (link)). The robust multi-array analysis (RMA) algorithm was used for background correction (28 (link)), and then quantile normalization was conducted (29 (link)). Cell of origin (COO) classification was determined primarily based on GEP data and secondarily on immunohistochemical results using the Visco-Young algorithm as described previously (5 (link)).
Gene set enrichment analysis was performed with GSEA application (Broad Institute at MIT, Cambridge, MA) using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway gene sets (186 gene sets). GSEA results with false discovery rate (FDR) ≤ 0.3 were considered to be significant.
Gene set enrichment analysis was performed with GSEA application (Broad Institute at MIT, Cambridge, MA) using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway gene sets (186 gene sets). GSEA results with false discovery rate (FDR) ≤ 0.3 were considered to be significant.
