Differential abundance and gene set enrichment in plasma of cancer patients versus controls

DESeq2 differential abundance output for genes with q < 0.05 and |log₂ fold change| > 1 in cancer vs control plasma samples:

• differentialabundance_pancancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in a pan-cancer plasma sample cohort (25 locally advanced to metastatic cancer types - 7 or 8 patients per type - vs 8 cancer-free control donors)
• differentialabundance_threecancer.txt: tables with differentially abundant genes (|log2(fold change)|>1 and adjusted p>0.05) per cancer-control comparison (cancertype) in the three-cancer plasma cohort (ovarian, prostate and uterine cancer - 11 or 12 patients per type - vs 20 cancer-free controls)
  • Gene_id: Ensembl gene id (GChr38 v91); baseMean: mean of normalized counts for all samples; log2FoldChange: log2 fold change for cancer vs control; lfcSE: standard error for cancer vs control; stat: Wald statistic for cancer vs control; pvalue: Wald test p-value for cancer vs control; padj: Benjamini-Hochberg corrected p-value; cancertype: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls.

Gene set enrichment analyses based on fold change ranked gene lists (cancer versus control) - results obtained with fgea (v1.22.0):

• customgenesets.txt: custom gene set lists based on RNA Atlas (&Human Protein Atlas), Tabula Sapiens, GTEX, TCGA data.
  • Reference: reference to create gene sets (including RNA Atlas, Human Protein Atlas, Tabula Sapiens, GTEX, and TCGA); set: set name; genes: gene list for set
• GSEA_pancancer.txt & GSEA_threecancer.txt: gene set enrichment results based on fold change ranked gene list (specific cancer type versus controls) in pan-cancer cohort and three-cancer cohort, respectively
  • Sets: gene set category (HALLMARK and KEGG: Hallmark and Canonical Pathways gene sets obtained from MSigDB (v2022.1); CUSTOM: custom tissue and cell type specific gene sets as defined in customgenesets.txt); pathway: pathway/set name; pval: enrichment p-value; padj: Benjamini-Hochberg adjusted p-value; log2err: expected error for the standard deviation of the P-value logarithm; ES: enrichment score, same as in Broad GSEA implementation; NES: enrichment score normalized to mean enrichment of random samples of the same size; size: size of the pathway after removing genes without statistic values; leadingEdge: leading edge genes that drive the enrichment; Disease: respective cancer type abbreviation of cancer patient plasma samples that were compared to plasma samples of controls