Meta-analysis of prostate cancer gene expression data identifies a novel discriminatory signature enriched for glycosylating enzymes

Table 5 A 71-gene signature capable of subclustering localised prostate cancer cases across multiple datasets

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
KEGG_PATHWAY	hsa04270:Vascular smooth muscle contraction	5	6.94	0	ACTG2, MYH11, KCNMB1, MYLK, MYL9	26	112	5085	8.73	0.12	0.12	1.99
KEGG_PATHWAY	hsa05414:Dilated cardiomyopathy	4	5.56	0.01	DES, PLN, IGF1, TPM2	26	92	5085	8.5	0.47	0.27	9.6
KEGG_PATHWAY	hsa04960:Aldosterone-regulated sodium reabsorption	3	4.17	0.02	IGF1, ATP1A2, IRS1	26	41	5085	14.31	0.66	0.31	15.92
KEGG_PATHWAY	hsa04310:Wnt signaling pathway	4	5.56	0.04	SFRP1, CAMK2G, PRICKLE2, MYC	26	151	5085	5.18	0.91	0.45	31.53
KEGG_PATHWAY	hsa05410:Hypertrophic cardiomyopathy (HCM)	3	4.17	0.06	DES, IGF1, TPM2	26	85	5085	6.9	0.99	0.57	49.28

A 71-gene signature representing a subset of genes from signature 1 (101.6.1). Columns 1 and 2 represent Affymetrix probe identifiers and gene symbols, respectively. Columns 3-5 represent probe signals in benign, localised prostate cancer and metastatic samples, respectively. Column 6 (‘primary.reporters) represents the differential probe signal between benign and localised prostate cancer cases with the associated p-values in column 7. Column 8 (‘metastatic.reporters’) represents the differential probe signal between metastatic and localised prostate cases with the associated p-values in column 9. Subsequent columns headed dist.0.6 through to dist.101.6 represent the gene signature codes for coexpressed genes at diminishing significance thresholds proceeding left-to-right across the table. All 71 genes form part of the same signature at all stringency thresholds and consequently the numbering in these columns for all genes is the same. Subsequent columns provide the gene location and gene name including information on chromosome number, cytogenetic band identifier and unigene accession codes. The same table layout is used in Additional files 2, 4, 5, 6, 7 and 8: Tables S1-S6.

ISSN: 1755-8794