Table 3.
Enriched Gene Sets: FEP vs HC.
| Gene set | Library | P-value | # | Genes |
|---|---|---|---|---|
| Kyoto Encyclopedia of Genes and Genomes | ||||
| Ribosome | KEGG | <0.001 | 46 | FAU, MRPL11, MRPL3, RPL17, RPL21, UBA52 |
| Oxidative phosphorylation | KEGG | <0.001 | 28 | ATP5C1, COX17, NDUFA1, PPA1, SDHD, UQCRH |
| Parkinson's disease | KEGG | <0.001 | 27 | ATP5C1, COX17, NDUFA1, PPA1, SDHD, UQCRH |
| Alzheimer's disease | KEGG | <0.001 | 26 | ATP5C1, COX17, NDUFA1, PPA1, SDHD, UQCRH |
| Huntington's disease | KEGG | 0.001 | 26 | ATP5C1, COX17, NDUFA1, PPA1, SDHD, UQCRH |
| Gene Ontology: Biological Process | ||||
| Cytokine production | GOBP | 0.007 | 14 | CASP1, CD46, G6PD, IL1B, PIK3CD, TBK1, TNFAIP8 |
| T cell receptor | GOBP | 0.009 | 16 | CARD11, CD3D, FYN, LAT, NCK1, RBCK1, UBE2N |
| Leukocyte activation | GOBP | 0.02 | 37 | AIF1, ANXA1, CD3E, CD48, CD7, CD79A, CD93, CXCR4, FYN, FZD7, GAPT, ITGAL, LAT, LYL1, SP3, VAMP7 |
| Regulation of NF-kB | GOBP | 0.041 | 25 | BIRC2, CARD11, CASP1, CD36, CXXC5, FYN, HSPB1, IL1B, IRF3, RBCK1, UBE2N |
| Defense response to Bacteria | GOBP | 0.043 | 11 | CAMP, CD36, DEFA1, FAU, HIST2H2BE, MYO1F, PGLYRP1, RPL39, TBK1, TNFAIP8 |
| Gene Ontology: Cellular Component | ||||
| Cytosol | GOCC | <0.001 | 238 | ATG3, BCR, DCP2, FYN, GMIP, GNAS, IL1B, IRF3, LYST, NDE1, NME1, PARK7, TBK1, UBA1, USP7 |
| Ribosomal subunit | GOCC | <0.001 | 45 | FAU, FXR2, MRPL3, RPL11, RPS15A, RPS3, RPS9 |
| Nucleolus | GOCC | <0.001 | 127 | AATF, CD79B, HIF1A, ILF3, IP6K1, JUND, NIN, PCNA, PTEN, RNF7, RPL11, STAT3, ZFR |
| Mitochondrion | GOCC | 0.002 | 90 | ATP5L, COQ5, COX7C, CYBB, ILF3, NME1, NUBPL, OAS2, PARK7, REXO2, TPP1, UCP2 |
| Lysosome | GOCC | 0.01 | 29 | CTNS, CTSA, CTSB, CTSZ, CXCR4, FUCA1, GALC, HEXB, LAT, SRGN, TPP1, USP4 |
| Gene Ontology: Biological Process | ||||
| Ribosome | GOMF | <0.001 | 45 | FAU, MRPL11, RPL27, RPS3, RPS3A, RPSA |
| Ion transport | GOMF | <0.001 | 18 | ATP5C1, ATP5E, COX6A1, NDUFA4, SLC9A1, UQCRH |
| Blood Module Library (WGCNA) | ||||
| Red Blood Cell | Blood | <0.001 | 170 | ADD3, BAT3, CD48, IL8RB, JUND, LAMP2, LDHA, LYST, MED1, PARK7, STAT3, TBK1, UBN1 |
| Blood Platelets | Blood | <0.001 | 39 | ACTN1, ANXA1, BCR, GNAS, GP9, JUND, LCN2, NRGN, TAGLN2, VCL |
| Brain Module Library (WGCNA) | ||||
| Post Synaptic Density Proteins | Brain | <0.001 | 133 | AGL, BAT3, BCR, FASN, FYN, G6PD, HGS, MSN, MTDH, MYH9, NME1, SEPT5, SND1, TAGLN2, TBK1, TLN1, TUBB2C, UBA1, VAMP2 |
| Pyramidal Neurons (Amygdala) | Brain | <0.001 | 37 | ACSL4, CRBN, DDR1, ENY2, GMFB, HDAC2, MATR3, NME1, PCNA, TBK1, UBE3A |
| Down in Alzheimer's | Brain | <0.001 | 80 | ACP1, ATP5O, ELMO1, GLO1, GMFB, GNAS, HEXB, ICA1, NME1, PARK7, STX7, TAF7, UBL3 |
| Glutamatergic synapse | Brain | <0.001 | 49 | ARF3, ATG3, BAT3, CABIN1, CENTB2, CPD, CTSD, DEK, GCA, GPR137, HGS, NRGN, PRNP, RARA, SPOCK2, SPTAN1, SRP9, TBCA, TIA1, UBE1, VAMP2 |
| CD40 stimulated Microglial cells | Brain | <0.001 | 58 | ACP1, BCR, CARM1, DDR1, FYN, ILF3, IRF3, NME1, SLC9A1, TRIM28, UBE2L3, VAMP2 |
Table of select gene sets enriched with differentially expressed (n = 978) genes between FEP and HC. P-values are Bonferroni corrected. Total number of DE genes present in each gene set are indicated in the # column. List of gene sets and gene symbols is not exhaustive, for complete results see supplementary table 2.
Table of select gene sets enriched with differentially expressed (n = 978) genes between FEP and HC. P-values are Bonferroni corrected. Total number of DE genes present in each gene set are indicated in the # column. List of gene sets and gene symbols is not exhaustive, for complete results see supplementary table 2.