Table 3. Gene set enrichment analysis of coexpression modules
Module (# genesa)Annotation setTermOverlapq‐valuebZ‐scoreCombined scorec
Sienna (370)GO Biological Process 2015Regulation of cytokine production28/4820.000268−2.5120.7
Positive regulation of cytokine production22/3270.000279−2.4520.1
Regulation of immune effector process18/2640.00106−2.4616.9
Reactome 2016Immune system65/15471.81e‐07−2.2334.7
Cytokine signaling in immune system26/6200.0211−2.399.21
WikiPathways 2016Type II interferon signaling (IFNG)6/375.35e‐05−1.8210.4
BDNF signaling pathway9/1440.00141−1.926.84
Senescence and autophagy in cancer8/1050.000720−1.776.72
Greenyellow (507)GO Biological Process 2015Negative regulation of smooth muscle cell migration4/120.223−2.653.97
Regulation of smooth muscle cell migration6/310.223−2.513.76
Endosome to lysosome transport5/310.662−2.611.08
Reactome 2016TNF signaling5/410.459−2.081.62
Deposition of new CENPA‐containing nucleosomes at the centromere5/520.459−2.041.59
Nucleosome assembly5/520.459−2.031.58
WikiPathways 2016Apoptosis modulation and signaling8/930.353−2.092.18
Complement and coagulation cascades6/590.353−1.901.98
Apoptosis modulation by HSP703/190.412−1.491.32
  • GO, gene ontology; IFNG, interferon‐gamma; BDNF, brain‐derived neurotrophic factor; TNF, tumor necrosis factor; CENPA, centromere protein A; HSP70, 70‐kilodalton heat shock protein.

  • a Number of unique gene symbols.

  • b q‐values are P‐values adjusted using the Benjamini–Hochberg method.

  • c Combined scores are the product of negative log P‐values and the Z‐score as described previously (Chen et al, 2013); the top three terms per annotation set, ordered by combined score, are displayed here.