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Table 1 Summary statistics of the differential transcription analysis, including 52 samples from 13 patients and 4 enriched cell types

From: Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression

Cell type Total genes Genes filtered (zeros) Genes filtered (PPC) Differentially transcribed Differentially transcribed in the interface (curated annotation)
Total (up/down) Of which cancer genes Of which PC genes Total (up/down) Of which cancer genes, consistent Of which PC genes, consistent
Epithelial 21,618 5408 189 171 (139/32) 45 (26%) 29 (64%) 80 (67/13) 35 (44%) 23 (67%)
Fibroblast 21,510 7141 651 267 (156/111) 27 (10%) 9 (33%) 97 (58/39) 17 (18%) 7 (41%)
Myeloid 22,507 13,836 2695 900 (827/73) 56 (6%) 11 (20%) 261 (238/23) 32 (12%) 10 (31%)
T cell 21,716 8807 540 288 (195/93) 42 (15%) 18 (42%) 83 (55/28) 26 (31%) 15 (58%)
  1. PPC posterior predictive check, PC prostate cancer. “Of which” refers to the gene selection relative to the category adjacent on the left. “Interface” refers to cell-surface and secreted protein-coding genes. “Curated” refers to the curated database for cellular-interface genes produced in our study (Supplementary file 2). “Consistent” refers to a consistent direction of transcriptional change according to the curated database. Genes were labelled as “cancer genes” if present in the tier1 COSMIC databasehttps://paperpile.com/c/BQQ95X/zLPNs [46] or labelled as such in our manually curated cell-type-specific database (Supplementary file 2). Genes were labelled as “prostate cancer genes” if present in the tier1 COSMIC prostate cancer database datasethttps://paperpile.com/c/BQQ95X/zLPNs [46] or labelled as such in our manually curated cell-type-specific database (Supplementary file 2)