Skip to main content

Table 2 WGCNA module summary and functional enrichments

From: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Module (gene number) Hub genes Viral Cor.* Enrichment terms Immune cell type enrichment
Pink (100) SPI1 0.83 GO:0006952 defense response (P adj = 6.17e-07) Neutrophils (P = 7.46e-11)
PLEK GO:0006955 immune response (P adj = 2.25e-06) Act. neutrophils (P = 4.44e-09)
HCK IPA path: Fcγ receptor-mediated phagocytosis in macrophages and monocytes (P = 4.97e-10) Eosinophils (P = 3.74e-04)
FGR IPA upstream regulator: IFNG (P = 4.77e-16) Act. macrophages (P = 9.78e-03)
TLR4 IPA function: leukocyte migration (increased) (P = 3.82e-22) Act. eosinophils (P = 2.67e-02)
Blue (726) SLAMF7 0.75 GO:0006955 immune response (P adj = 5.31e-76) Act. macrophages (P = 2.49e-16)
SP100 GO:0006952 defense response (P adj = 2.15e-29) Dendritic cells (P = 3.01e-11)
DTX3L GO:0045321 leukocyte activation (P adj = 3.79e-26) Act. neutrophils (P = 3.78e-05)
GIMAP4 IPA upstream regulator: IFNG (P = 1.66e-100) Neutrophils (P = 1.99e-04)
OAS3 IPA path: interferon signaling (P = 3.35e-22) NK cells (P = 2.64e-02)
Black (117) DCAKD 0.28 GO:0031982 ~ vesicle (P adj = 1.38e-02) Act. macrophages (P = 4.06e-03)
GNA13 GO:0012505 endomembrane system (P adj = 2.10e-02)
PICALM IPA upstream regulator: CHEK2 (P = 6.49e-05)
CREB1 IPA path: ephrin receptor signaling (P = 3.26e-04)
LARP4 IPA function: viral infection (increased) (P = 1.02e-04)
Magenta (85) TNKS2 0.32 No significant DAVID enrichments Act. macrophages (P = 4.57e-02)
VCPIP1 IPA path: oxidative phosphorylation (P = 8.05e-05)
MIER1 IPA path: mitochondrial dysfunction (P = 6.51e-04)
CD2AP IPA path: NF-κB signaling (P = 6.14e-03)
ARAP2  
Yellow (189) CHST9 0.70 No significant DAVID enrichments Act. neutrophils (P = 4.00e-04)
ITGA5 IPA function: inflammatory response (P = 2.09e-11) Act. macrophages (P = 9.78e-03)
C8orf47 IPA function: quantity of leukocytes (P = 1.67e-10) Neutrophils (P = 1.56e-02)
OXSR1 IPA function: differentiation of cells (P = 1.74e-10) Act. eosinophils (P = 1.83e-02)
ITPRIPL2   
Green (179) RPL10A −0.46 GO:0006414 translational elongation (P adj = 3.65e-44) B cells (P adj = 1.07e-07)
RPL3 KEGG: hsa03010 ribosome (P adj = 3.34e-37) Th2 cells (P adj = 8.30e-05)
EEF2 GO:0006412 translation (P adj = 7.72e-36) T cells (P adj = 2.33e-04)
RPS14 IPA path: eIF2 signaling (P = 4.07e-47) Mast cells (P adj = 1.33e-03)
RPL4   Th1 cells (P adj = 2.42e-02)
Brown (203) ELOVL5 −0.74 Type 2 inflammation (P = 3.30e-04) No significant immune cell enrichments
CDH26 No significant DAVID enrichments
ALOX15 IPA upstream regulator: IL13 (P = 2.77e-05)
FETUB  
VWF  
Red (164) CFL1 0.50 GO:0015629 actin cytoskeleton (P adj = 2.41e-06) Act. neutrophils (P adj = 2.35e-02)
CAP1 GO:0031252 cell leading edge (P adj = 6.68e-05) Act. macrophages (P adj = 3.04e-02)
VASP IPA path: remodeling of epithelial adherens junctions (P = 2.42e-09)  
DIAPH1 IPA upstream predictor: TGFB1 (P = 6.88e-09)  
TMBIM1 IPA function: organization of cytoskeleton (increased) (P = 3.65e-15)  
Turquoise (1,615) C6orf165 −0.43 GO:0005929 cilium (P adj = 2.78e-30) No significant immune cell enrichments
ARMC2 GO:0015630 microtubule cytoskeleton (P adj = 1.02e-23)
CAPSL GO:0005930 axoneme (P = 3.01e-21)
EFCAB6 IPA upstream regulator: RFX3 (P = 1.74e-05)
ANKRD66 IPA function: formation of cilia (decreased) (P = 1.47e-43)
  1. *Cor = Spearman correlation of module eigengenes with depth of detected viral genomes (for virus high samples only)