Table 2. Summary of the total number of BMKs identified per differential expression analysis (padj<0.01) or multivariate analysis and those selected for validation in the discovery set or confirmed in the validation set.

Biomarker selection in discovery set	Patients considered	Number of identified BMKs (padj<0.01)	Number of selected BMKs
Univariate (DEGs)		1,016	450
CRC I-IV vs CON	S+K ∩ S	341	341
CRC I-IV vs CON	S	430	89
HG AA vs CON	S+K	2*	2
HG AA vs CON	S	2*	1
CRIC I-II vs CON	S	115	13
CRC I-II-III vs CON	S	128	4
Multivariate		141	74
Voom	S+K	16	8
glmnet	S+K	15	10
NSC	S+K	90	41
Evolutionary random forest	S+K	20	15
Total unique BMKs			524

Analyses performed on validation set	Patients considered	Number of identified BMKs (padj<0.01)	Number of confirmed BMKs
Univariate (DEGs)		3,733	212
CON vs CRC	S+K ∩ S	614	124
CON vs CRC	S	715	3
CON vs AA	S+K ∩ S	10	1
CON vs CRC I-II	S+K ∪ S	601	24
CON vs CRC I-II-III	S+K ∪ S	852	19
CON vs CRC	S+K ∪ S	324**	16
CON vs CRC III-IV	S+K ∪ S	617**	25
Multivariate		345	14
Voom	S+K	97	2
NSC	S+K	159	0
glmnet	S+K	89	12
Total unique BMKs			226

New BMKs were added to the selection pool subsequently in the discovery set. S=Swiss samples only, K=Korean samples only. *padj, **DEGs confirmed with absolute log2 fold change regardless of padj on validation set.

*padj<0.05.

**DEGs confirmed with absolute log2 fold change >0.5 or <−0.5 regardless of padj on validation set.

AAadvanced adenomaBMKbiomarkerCONcontrol subjectsCRCcolorectal cancer DEGdifferential expressed geneKKoreanNSCnearest shrunken centroidspadjadjusted p valueSSwiss