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. 2024 Nov 21;12(11):e009888. doi: 10.1136/jitc-2024-009888

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