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

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

Cell type	Total genes	Genes filtered (zeros)	Genes filtered (PPC)	Differentially transcribed			Differentially transcribed in the interface (curated annotation)
Cell type	Total genes	Genes filtered (zeros)	Genes filtered (PPC)	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%)

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)

ISSN: 1471-2407