Supplementary Table 2.
The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes (DEGs) in protein–protein interaction (PPI) sub-modules (top 5).
| Names | Terms | Gene count | P-value | Gene symbols |
|---|---|---|---|---|
| Group1_sub-module 1 | Ribosome | 28 | 2.78E-62 | PRL19, RPL37A, RPL23A, RPL22, RPL3, RPL32, RPL35A, RPL7, PRS18, RPS19, RPS12, RPS23, RPS3, RPS15A, RPL30, RPL14, RPL38, RPL15, RPL10A, RPL8, RPL12, RPL11, RPS16, RPS4X, RPS5, RPS28, RPS25 |
| Thyroid cancer | 1 | 0.025 | MYC | |
| Bladder cancer | 1 | 0.035 | MYC | |
| Endometrial cancer | 1 | 0.044 | MYC | |
| Acute myeloid leukemia | 1 | 0.048 | MYC | |
| Group1_sub-module 2 | RNA transport | 9 | 3.35E-18 | PABPC1, EIF3A, EIF3B, EIF3D, EIF3F, EIF3G, EIF3H, EIF3I, EIF4B |
| Malaria | 1 | 0.0187 | CD81 | |
| B cell receptor signaling pathway | 1 | 0.0276 | CD81 | |
| RNA degradation | 1 | 0.0290 | PABPC1 | |
| mRNA surveillance pathway | 1 | 0.0345 | PABPC1 | |
| Group1_sub-module 3 | RNA degradation | 9 | 6.46E-18 | EXOSC1, EXOSC4, EXOSC5, EXOSC6, EXOSC7, EXOSC8, EXOSC9, EXOSC10, SKIV2L2 |
| Spliceosome | 5 | 5.37E-08 | EIF4A3, PRPF19, SF3A1, SF3A2, SF3A3 | |
| Ribosome biogenesis in eukaryotes | 2 | 0.0020 | UTP14A, GTPBP4 | |
| Rap1 signaling pathway | 2 | 0.0105 | TIAM1, SIPA1L1 | |
| MicroRNAs in cancer | 2 | 0.0202 | CDC25B, HDAC4 | |
| Group1_sub-module 4 | Spliceosome | 3 | 1.11E-05 | LSM4, LSM8, PPIH |
| RNA degradation | 2 | 0.0003 | LSM4, LSM8 | |
| RNA polymerase | 1 | 0.0107 | POLR2D | |
| Basal transcription factors | 1 | 0.0149 | TAF1 | |
| Pyrimidine metabolism | 1 | 0.0341 | POLR2D | |
| Group2_sub-module 1 | – | – | – | |
| Group2_sub-module 2 | Cell cycle | 2 | 0.0128 | TP53, CDC25B |
| MAPK signaling pathway | 4 | 0.0003 | TP53, CDC25B, MAX, ARRB2 | |
| MicroRNAs in cancer | 4 | 0.0007 | TP53, CDC25B, HDAC4, HNRNPK | |
| Viral carcinogenesis | 3 | 0.0029 | TP53, HDAC4, HNRNPK | |
| Chronic myeloid leukemia | 2 | 0.0047 | TP53, GAB2 | |
| Group2_sub-module 3 | Spliceosome | 7 | 3.76E-12 | HNRNPA3, U2AF1, SF3A1, PRPF19, SNRPA1, DHX15, DDX5 |
| Oocyte meiosis | 2 | 0.0030 | CDC25C, YWHAQ | |
| Cell cycle | 2 | 0.0031 | CDC25C, YWHAQ | |
| Pathogenic Escherichia coli infection | 1 | 0.0360 | YWHAQ | |
| Shigellosis | 1 | 0.0423 | U2AF1 | |
| Group2_sub-module 4 | Spliceosome | 2 | 0.0006 | PCBP1, HNRNP |
| Ribosome | 2 | 0.0007 | RPS27L, RPS28 | |
| PI3K-Akt signaling pathway | 2 | 0.0039 | ITGA4, BRCA1 | |
| Intestinal immune network for IgA production | 1 | 0.0140 | ITGA4 | |
| Legionellosis | 1 | 0.0154 | EEF1A1 | |
| Group2_sub-module 5 | Cell cycle | 1 | 0.1849 | BUB3 |
| RNA degradation | 6 | 5.10E-09 | EXOSC6, DIS3L, EXOSC4, EXOSC8, EXOSC5, EXOSC7 | |
| Spliceosome | 6 | 1.18E-07 | SRSF7, PRPF3, SNRNP40, PPIE, SNRPE, SF3A2 | |
| Proteasome | 4 | 1.19E-06 | PSMD6, PSMD7, PSMB6, PSMD12 | |
| Ribosome | 5 | 3.86E-06 | MRPL10, MRPS14, MRPL30, MRPL4, MRPL28 | |
| Group2_sub-module 6 | Axon guidance | 3 | 0.0005 | CFL1, KRAS, EPHA2 |
| Cell cycle | 2 | 0.0055 | CDKN2C, CDK4 | |
| Endocrine resistance | 3 | 9.50E-05 | CDKN2C, CDK4, KRAS | |
| PI3K-Akt signaling pathway | 4 | 0.0002 | KRAS, CDK4, FGFR4, EPHA2 | |
| Signaling pathways regulating pluripotency of stem cells | 3 | 0.0003C | SOX2, KRAS, FGFR4 | |
| Group2_sub-module 7 | DNA replication | 3 | 0.0001 | RFC5, RFC1, SSBP1 |
| RNA transport | 6 | 5.79E-06 | EIF1B, EIF3A, EIF3C, EIF3D, EIF3J, SRRM1 | |
| Proteasome | 4 | 6.41E-06 | PSMC4, PSMB5, PSME1, PSMD1 | |
| Nucleotide excision repair | 4 | 8.18E-06 | RFC5, RFC1, XPC, ERCC6 | |
| Cell cycle | 1 | 0.2675 | CCND1 | |
| Group2_sub-module 8 | Cell cycle | 4 | 0.0005 | E2F1, SMC1A, TFDP1, MCM3 |
| Metabolic pathways | 19 | 3.30E-09 | DNMT3A, CYC1, B3GNT2, ALDH18A1, PFAS, SORD, MOGS, SMS, POLR3D, MAN2A1, NAGK, POLE3, POLR1D, LDHAL6B, POLR3C, SDHA, NTPCR, PFKP, DLST | |
| Purine metabolism | 7 | 1.04E-06 | PNPT1, PFAS, POLR3D, NTPCR, POLE3, POLR1D, POLR3C | |
| Pyrimidine metabolism | 5 | 1.68E-05 | POLE3, POLR3C, PNPT1, POLR1D, POLR3D | |
| RNA polymerase | 3 | 0.0001 | POLR3C, POLR1D, POLR3D | |
| Group3_sub-module 1 | Transcriptional misregulation in cancer | 2 | 0.0011 | BCL6, ZBTB16 |
| Nicotinate and nicotinamide metabolism | 1 | 0.0085 | NADK | |
| Acute myeloid leukemia | 1 | 0.0159 | ZBTB16 | |
| Fc epsilon RI signaling pathway | 1 | 0.0189 | GAB2 | |
| Chronic myeloid leukemia | 1 | 0.0203 | GAB2 | |
| Group3_sub-module 2 | Endocytosis | 4 | 6.04E-07 | CLTB,ARF1,IGF2R,AP2M1 |
| Protein processing in endoplasmic reticulum | 3 | 1.21E-05 | SEC24C,SEC23B,MAN1A1 | |
| Endocrine and other factor-regulated calcium reabsorption | 2 | 8.12E-05 | CLTB,AP2M1 | |
| Legionellosis | 2 | 0.0001 | RAB1A,ARF1 | |
| Synaptic vesicle cycle | 2 | 0.0001 | CLTB,AP2M1 | |
| Group3_sub-module 3 | Hippo signaling pathway -multiple species | 3 | 9.45E-09 | SAV1, RASSF1,LATS2 |
| Hippo signaling pathway | 3 | 1.20E-06 | SAV1, RASSF1,LATS2 | |
| Ras signaling pathway | 2 | 0.0004 | RASSF1,MET | |
| MicroRNAs in cancer | 2 | 0.0008 | RASSF1,MET | |
| Pathways in cancer | 2 | 0.0015 | RASSF1,MET | |
| Group4_sub-module | Thyroid hormone signaling pathway | 1 | 0.0149 | MED30 |
Group 1: the blood samples of sepsis and healthy controls; Group 2: the blood samples of septic shock and healthy controls; Group 3: the neutrophil samples of sepsis and normal controls; Group 4: the neutrophil samples of septic and normal controls.