Table 2.
Summary of Gene Modules That Are Significantly Related to Sepsis in Weighted Gene Coexpression Network Analysis
| Module | Genes (n) | Hub Genes | Ten Most Differentially Expressed Genes | Variables (ρ*,P Value) | Enriched Terms | |
|---|---|---|---|---|---|---|
| grey60 | 225 | C1R, CNN3, CSDA, ICAM1, IFITM2, PXDC1, SHC1, STAT3, TMBIM1, and TNFRSF1A | BCL3, IER3, S100A8, SHC1, IL15RA, TNFRSF1A, ANGPTL4, PNP, S100A9, and IL6 | Sepsis | (0.51, 0.01) | Cytokine-mediated signaling†, inflammatory response†, response to external stimulus†, and cell death† |
| RIN | (0.27, 0.2) | |||||
| Braak | (0.0057, 0.8) | |||||
| CERAD | (0.13, 0.6) | |||||
| Age | (0.43, 0.04) | |||||
| midnightblue | 259 | BAI1, CACNA1I, DUSP8, GLIS1, ITSN1, MLLT1, NEURL, PALM, PITPNM2, and PLEKHA6 | PRB1, YAP1, RHOF, INPP5E, TRIM7, TRAF7, ZC3HAV1, INTU, ASIC4, and PHLDA1 | Sepsis | (0.41, 0.05) | Synapse‡, actin cytoskeleton process‡, dendritic tree§, voltage-gated calcium channel§, and glycerophospholipid synthetic process§ |
| RIN | (0.54, 0.008) | |||||
| Braak | (0.068, 0.8) | |||||
| CERAD | (0.099, 0.7) | |||||
| Age | (0.063, 0.8) | |||||
| darkorange | 63 | AFF1, ASB15, EVC2, HMGB2, IL16, INPP5E, LRP2BP, SERP1, UTS2R, and WFIKKN1 | FOSL1, LOC643733, LOC649330, GJA4, WNT8B, FAM181A-AS1, LRRC43, LOC100505835, HMBG2, and LAG3 | Sepsis | (0.53, 0.009) | DNA binding‖ and regulation of transforming growth factor β signaling‖ |
| RIN | (0.52, 0.01) | |||||
| Braak | (0.051, 0.8) | |||||
| CERAD | (0.26, 0.2) | |||||
| Age | (0.039, 0.9) | |||||
| lightgreen | 213 | ADSS, CDK17, KIAA1244, LANCL1, LPGAT1, MTMR2, PAPSS1, SPTLC1, TBCB, and USP32 | SNX30, MFSD6, ACAT2, HSD17B4, NIPA1, ST3GAL5, PCYT2, SCHIP1, TUBGCP3, and ABHD5 | Sepsis | (0.45, 0.03) | COPI-coated vesicle membrane§, cholesterol biosynthesis‖, and protein glycosylation‖ |
| RIN | (0.66; 5 × 10−7) | |||||
| Braak | (0.069, 0.8) | |||||
| CERAD | (0.12, 0.6) | |||||
| Age | (0.14, 0.5) | |||||
| skyblue | 54 | B4GALNT1, DZIP1, GOLGA7B, GPR162, IQUB, KIAA1522, MAST1, MCF2L2, PSD, and RHOF | FZD4, ATP6V0A4, SRP14, GRHL1, GOLGA7B, LGALS3, ANKRD36BP2, SLC10A1, EPB41L5, and SPRY1 | Sepsis | (0.52, 0.01) | Regulation of adenylate cyclase activity involved in G protein–coupled receptor signaling pathway‖, and regulation of neurofibrillary tangle assembly‖ |
| RIN | (0.32, 0.1) | |||||
| Braak | (0.19, 0.4) | |||||
| CERAD | (0.085, 0.7) | |||||
| Age | (0.078, 0.7) | |||||
| paleturquoise | 49 | AFF1, DTNA, LRRC37B, MCL1, PLIN2, SAT1, SOX9, TGFBR3, UBR5, and ZNF395 | METRNL, GNA14, FNDC3B, GPR4, ZC2HC1C, MCL1, SERP1, IL18R1, SAT1, and SCN9A | Sepsis | (0.46, 0.03) | CD4 receptor binding‡, T-cell cytokine production‖, IL-1 receptor activity‖, and protein ubiquitination‖ |
| RIN | (0.56, 0.005) | |||||
| Braak | (0.025, 0.9) | |||||
| CERAD | (0.081, 0.7) | |||||
| Age | (0.3, 0.2) | |||||
Definition of abbreviations: CERAD = Consortium to Establish a Registry for Alzheimer’s Disease score; RIN = RNA integrity number.
Hub genes are determined by correlation between the expression of an individual gene and the eigengene of each module and reflect connectivity of the gene to expression of the module as a whole. Top differentially expressed genes were determined by cross-referencing module membership with differential expression calculated from the dataset as a whole. Gene enrichment analysis was performed on modules that were significantly correlated with sepsis using the enrichment analysis tool within the weighted gene coexpression network analysis and with the bioinformatics tool DAVID (14).
Absolute value of biweight-mid correlation between the variable of interest and the module eigengene.
P < 1 × 10−10.
P < 1 × 10−5.
P < 1 × 10−4.
P < 0.01.