Table 1.

Overlap of DEGs identified in the lowest LRRK2-expressing TCGA LUAD tumors with DEGs identified in mouse lung development.

Developmental time points	Mouse lung development DEG list	Gene count a	LUAD DEG list	Gene count	Observed gene intersectionb	Simulated gene intersection (min–max)	Empirical P-valuec	Observed > Simulated intersection?d
E11.5–12.5 vs E13.5-E15.5	EMB vs PSG ↑	1335	Lowest LRRK2 vs Highest LRRK2 (↑)	1302	88	32–102	0.0014	No
E11.5–12.5 vs E13.5-E15.5	EMB vs PSG ↓	190	Lowest LRRK2 vs Highest LRRK2 (↓)	2199	27	2–35	0.0018	No
E13.5-E15.5 vs E16.5-E17.5	PSG vs CAN ↑	1021	↑	1302	40	23–87	0.91	No
E13.5-E15.5 vs E16.5-E17.5	PSG vs CAN ↓	757	↓	2199	45	32–96	0.99	No
E16.5-E17.5 vs E18.5_E19.5	CAN vs SAC ↑	853	↑	1302	31	18–70	0.95	No
E16.5-E17.5 vs E18.5_E19.5	CAN vs SAC ↓	806	↓	2199	26	36–102	1.00	No
E18.5_E19.5 vs P0-P3	SAC vs ALV1 ↑	855	↑	1302	45	17–70	0.25	No
E18.5_E19.5 vs P0-P3	SAC vs ALV1 ↓	594	↓	2199	59	23–77	0.055	No
P0-P3 vs P4-P7	ALV1 vs ALV2 ↑	473	↑	1302	208	6–46	< 0.0001	Yes
P0-P3 vs P4-P7	ALV1 vs ALV2 ↓	692	↓	2199	252	27–89	< 0.0001	Yes
P4-P7 vs P9-P12	ALV2 vs ALV3 ↑	273	↑	1302	15	0–30	0.25	No
P4-P7 vs P9-P12	ALV2 vs ALV3 ↓	371	↓	2199	25	11–57	0.82	No
P9-P12 vs P13-P18	ALV3 vs ALV4 ↑	592	↑	1302	18	10–56	0.98	No
P9-P12 vs P13-P18	ALV3 vs ALV4 ↓	623	↓	2199	85	24–84	< 0.0001	Yes
P13-P18 vs P21-P56	ALV4 vs MAT ↑	836	↑	1302	63	16–70	0.00030	No
P13-P18 vs P21-P56	ALV4 vs MAT ↓	643	↓	2199	139	27–83	< 0.0001	Yes

↑/↓ increased/decreased, EMB embryonic, PSG pseudoglandular, CAN canalicular, SAC saccular, ALV1-4 alveolarization stages 1–4, MAT mature lung.

^aGene count is defined as the count of differentially increased or decreased genes, identified in lung development stage comparisons by Beauchemin et al.⁴⁴ or in this study.

^bObserved gene intersection was calculated as the count of shared DEGs, per comparison.

^cEmpirical p-value was calculated per gene intersection as p = (b + 1)/(m + 1), where: b was the number of times a simulated gene intersection was ≥ the observed gene intersection and m was the number of permutations (m = 100,000) (Bonferroni adjP < 0.003 for 16 comparisons).

^d’yes’ and bold rows indicate that the observed gene intersection was greater than the maximum simulated gene intersection.