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

From: An integrative network-based approach to identify driving gene communities in chronic obstructive pulmonary disease

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

  1. 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).
  2. COPD chronic obstructive pulmonary disease, MSigDB molecular signatures database, NS not significant.
  3. *p value was significant in more than 80% of the iterations but floating.
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