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Table 4 Populated upstream regulatory networks

From: Transcriptomic evidence of a para-inflammatory state in the middle aged lumbar spinal cord

Upstream Regulator Molecule Type p-value of overlap Target molecules in dataset Mechanistic Network
IFNG Pro-inflammatory cytokine produced mainly by activated T cells 1.33E-16 ABCA1,AIF1,ASS1,AVPR1A,BLNK,C1QA,C1QB,C1QC,C3,C4A/C4B,CCND2,CD163,CD74,CDH22,Cebpd,CP,CTGF,FAM107A,FCER1G,FCGR2B,FCGR3A,HLA-DQA1,HLADRA,HMGCR,HMGCS1,IDI1,IFITM1,IGF1,ITGB2,LGALS3,MAP3K8,MERTK,MT1E,PHACTR1,PLEK,PPARGC1B,RT1EC2,SERPING1,SLC6A6,SLC9A3,STAT6,TIMP1,TLR7,TREM2,TYROBP CEBPA,FOXO3,Hdac,IFNG,IL1B,IL4,LDL,NFkBcomplex,PPARG,RUNX2,SP1,SP3,STAT1,STAT3,STAT5a/b,STAT6,TNF
Inosine Metabolite with immunomodulatory effects 4.15E-16 AIF1,ANXA1,C1QA,C1QB,C1QC,C1S,C3,C4A/B,CFD,MS4a6b,MT1E,SERPING1,TIMP1  
LPS Major component of outer membrane of Gram-negative bacteria 2.92E-14 ABCA1,ANXA1,ANXA3,ASAP1,ASS1,AVPR1A,BMP2,C3,CCND2,CD163,CD37,CD53,CD74,CFD,CP,CSF3R,CTGF,DDX6,DIO2,EMR1,FCER1G,FCGR2B,Gp49a/Lilrb4,HLADQA1,IFITM1,IGF1,ITGB2,LGALS3,MAFF,MAP3K8,MERTK,MMP14,MT1E,MT1H,PDE4B,PLD4,PLEK,PPARGC1B,PYCARD,SLC9A3,SLFN13,STAT6,TIMP1,TLR7,TNFSF4,TREM2,TYROBP,VEZF1 CEBPA,FOXO3,HDAC,IFNG,IL1B,IL4,IL6,NCOA1,NFkB (complex),PPARG,RUNX2,SP1,SP3,STAT1,STAT3,STAT4,STAT5a/b,STAT6,TNF,lipopolysaccharide
DYSF Ca2+ sensor protein involved in synaptic vesicle fusion 4.36E-12 ABCA1,ANXA1,C1QB,CD53,CD74,CFD,FCGR2B,GP49a/Lilrb4,HLA-DQA1,LGALS3,LYZ1/LYZ2,TIMP1  
Vancomycin Antibiotic that exhibits significant neurotoxicity 8.00E-12 ANXA1,C3,C4A/C4B,CP,FMO2,GPNMB,LGALS3,MS4a6b,S100A11,SCD,TIMP1,TMEM173  
TNF Pro-inflammatory cytokine; In the CNS, derived mainly from activated microglia 2.31E-11 ABCA1,ANXA1,ASS1,AVPR1A,BIRC7,BMP2,C3,CCND2,CD163,Cebpd,CFD,CP,CTGF,FCER1G,FCGR2B,HERC1,HLADRA,HMGCR,HSD17B7,IFITM1,IGF1,ITGB2,LGALS3,LRG1,LSS,MAFF,MAP3K8,MMP14,MT1E,MT1H,PDE4B,PER2,POSTN,PPARGC1B,PYCARD,RGS4,SCD,SLC9A3,TIMP1,TLR7,TNR,TREM2 CEBPA,CTNNB1,FOXO3,IFNG,IL1B,IL4,NFkB complex),PI3K complex,SP1,SP3,STAT1,STAT3,STAT5a/b,STAT6,TNF,estrogen receptor
  1. Members of the annotated differential gene set (353) were fit to regulatory networks in the IPA data base. P values are the probability that the observed overlap occurred by chance alone