Table 1.

Top pathway models for lung adenocarcinoma

Consensus cancer genes			All TCGA genes
#	Gene set	$R_{\mathit{\text{pred}}}^2$	#	Gene set	$R_{\mathit{\text{pred}}}^2$
1	BIOCARTA_RANMS_PATHWAY	0.487	1	BIOCARTA_RANMS_PATHWAY	0.465
2	REACTOME_ACTIVATION_OF_ATR_IN_RESPO...	0.486	3	REACTOME_G2_M_CHECKPOINTS	0.459
3	REACTOME_G2_M_CHECKPOINTS	0.483	2	REACTOME_ACTIVATION_OF_ATR_IN_RESPO...	0.456
4	REACTOME_CELL_CYCLE	0.472	6	REACTOME_CDC6_ASSOCIATION_WITH_THE_...	0.450
5	REACTOME_MITOTIC_M_M_G1_PHASES	0.468	14	REACTOME_CHROMOSOME_MAINTENANCE	0.434
6	REACTOME_CDC6_ASSOCIATION_WITH_THE_...	0.468	9	REACTOME_G0_AND_EARLY_G1	0.433
7	REACTOME_DNA_REPLICATION	0.464	4	REACTOME_CELL_CYCLE	0.431
8	REACTOME_CELL_CYCLE_MITOTIC	0.464	8	REACTOME_CELL_CYCLE_MITOTIC	0.429
9	REACTOME_G0_AND_EARLY_G1	0.454	5	REACTOME_MITOTIC_M_M_G1_PHASES	0.428
10	PID_ATR_PATHWAY	0.450	7	REACTOME_DNA_REPLICATION	0.427

Top ten MSigDB C2.CP pathways ranked according to $R_{\mathit{\text{pred}}}^2$ for regression models constructed using the TCGA lung adenocarcinoma data. Separate rankings are shown for models estimated using both potential predictor sets (i.e., the somatic alterations for either genes in the COSMIC cancer gene census or all genes available in the TCGA data). The "#" columns contain the pathway rank according to the COSMIC models. Note that the complete names of the rank 2 and rank 6 pathways for COSMIC genes are REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS and REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX