Table 2.

Comparison of enriched pathways and biological processes (annotated by Hallmark molecular signatures database) at COPD stable-state and exacerbation conditions in presence or absence of bacterial infection

Pathways and biological processes (Hallmark MSigDB)	Hallmark MSigDB systematic name	Exacerbation, Bacteria-negative, average p value (88 samples)	Exacerbation, Bacteria-positive, average p value (146 samples)	Stable, Bacteria-negative, average p value (63 samples)	Stable, Bacteria-positive, average p value (79 samples)
E2F_TARGETS	M5925	NS	10-5	NS	NS
ESTROGEN_RESPONSE_EARLY	M5906	NS	7•10-3	NS	NS
ESTROGEN_RESPONSE_LATE	M5907	NS	6•10-4	NS	NS
G2M_CHECKPOINT	M5901	NS	10-7	NS	NS
HEME_METABOLISM	M5945	5•10-4	6•10-3	5•10-4	5•10-4
INTERFERON_ALPHA_RESPONSE	M5911	2•10-6*	10-6*	NS	2•10-4*
INTERFERON_GAMMA_RESPONSE	M5913	5•10-10*	8•10-7*	NS	2•10-4*
KRAS_SIGNALING_DN	M5956	NS	4•10-3*	NS	NS
MITOTIC_SPINDLE	M5893	NS	10-3	NS	NS
OXIDATIVE_PHOSPHORYLATION	M5936	NS	2•10-3	NS	2•10-3

Results of the multi-network gene community detection (MNGCD) analysis reported separately for stable-state and exacerbation conditions combined with presence (positive) and absence (negative) of bacterial infection. The p values of the hypergeometric enrichment are corrected by Benjamini-Hochberg method (significance p < 0.01). For multiple communities enriched with the same Hallmark term, the minimum p value for that repetition was taken and p values of the 20 iterations were then log-averaged (details in Supplementary information section 3).

COPD chronic obstructive pulmonary disease, MSigDB molecular signatures database, NS not significant.

*p value was significant in more than 80% of the iterations but floating.