Table 3. Open in new tab Enrichment...

Table 3.

Enrichment analysis results for BRCA subtyping.^a

Subtype	N $_{LASSO}$	N $_{w_{GIS}}$	N $_{s h a r e d}$	GO $_{LASSO}$	GO $_{w_{GIS}}$	Reactome $_{LASSO}$	Reactome $_{w_{GIS}}$	HPO $_{LASSO}$	HPO $_{w_{GIS}}$
Basal	30	30	25	1564 (8.0%)	1871 [1.20] (16.0%^b)	104 (0%)	105 [1.01] (0%)	967 (0%)	1182 [1.22] (0%)
Her2	51	56	46	2376 (0%)	2685 [1.13] (1.4%^b)	361 (0.8%)	381 [1.06] (0.8%)	921 (0%)	1346 [1.46] (0.2%^b)
LumA	76	86	71	2747 (6.2%)	3159 [1.15] (7.7%^b)	346 (12.7%)	495 [1.43] (12.5%)	1519 (1.1%)	1980 [1.30] (3.7%)
LumB	57	63	53	2267 (1.3%)	2518 [1.11] (1.2%)	164 (5.5%)	245 [1.49] (3.7%)	1165 (7.9%)	1602 [1.38] (9.2%)

Subtype	N $_{LASSO}$	N $_{w_{GIS}}$	N $_{s h a r e d}$	GO $_{LASSO}$	GO $_{w_{GIS}}$	Reactome $_{LASSO}$	Reactome $_{w_{GIS}}$	HPO $_{LASSO}$	HPO $_{w_{GIS}}$
Basal	30	30	25	1564 (8.0%)	1871 [1.20] (16.0%^b)	104 (0%)	105 [1.01] (0%)	967 (0%)	1182 [1.22] (0%)
Her2	51	56	46	2376 (0%)	2685 [1.13] (1.4%^b)	361 (0.8%)	381 [1.06] (0.8%)	921 (0%)	1346 [1.46] (0.2%^b)
LumA	76	86	71	2747 (6.2%)	3159 [1.15] (7.7%^b)	346 (12.7%)	495 [1.43] (12.5%)	1519 (1.1%)	1980 [1.30] (3.7%)
LumB	57	63	53	2267 (1.3%)	2518 [1.11] (1.2%)	164 (5.5%)	245 [1.49] (3.7%)	1165 (7.9%)	1602 [1.38] (9.2%)

Number of GO, reactome biological pathway, or HPO annotation terms retrieved for each selected feature subset of size N (and percentage of significantly enriched terms, with FDR P-value $<$ 0.05). $w_{GIS}$ refers to GIS-weighted LASSO, with penalty as in Equation (8). $[\cdot]$ ⁠: ratio between the number of retrieved terms annotated to the gene subsets selected by the GIS-weighted and standard LASSO regularization.

Statistically significant percentage of enriched terms with respect to the standard LASSO-related ones (Z-test for proportions, P-value $<$ 0.05).

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