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Table 1 Twenty-seven focused pathways that significantly changed the internal gene-gene expression correlation in CKD advancement

From: Expression correlation attenuates within and between key signaling pathways in chronic kidney disease

Pathway Aggregated p CKD RNA-Seq GSE62792 GSE37171
p Early Late p Normal Disease p Normal Disease
Regulation of nuclear SMAD2/3 signaling 4.13E-06 0.012 FOXO1 MAX 0.001 HNF4A TCF3 0.002 SMAD2 FOXO1
CD4 T cell receptor signaling 4.74E-06 0.014 HLA-DPB1 NFKB1 0.001 HLA-DPA1 PPP3CC 0.002 MAP 3 K7 CD247
TCR signaling in naive CD4+ T cells 5.93E-06 0.018 PTPRC CBL 0.001 CD3D IKBKB 0.002 RASSF5 CD247
IL2 signaling events mediated by STAT5 1.07E-05 0.001 BCL2 BCL2 0.010 GRB2 CDK6 0.007 SHC1 CCND2
Angiopoietin receptor Tie2-mediated signaling 1.82E-05 0.001 FOXO1 NFKB1 0.002 AKT1 RAC1 0.064 FOXO1 MAPK1
TRAIL signaling pathway 1.87E-05 0.033 TNFSF10 TNFRSF10D 0.002 FADD DAP3 0.002 PIK3CA MAPK1
Signaling events mediated by HDAC Class II 2.46E-05 0.030 HSP90AA1 GNB1 0.001 NUP214 BCOR 0.006 GNB1 RAN
Neurotrophic factor-mediated Trk receptor signaling 3.22E-05 0.061 STAT3 RAP1B 0.001 MAPK3 RAPGEF1 0.004 RHOA RHOA
Canonical Wnt signaling pathway Diagram 3.41E-05 0.009 GSK3B FZD5 0.001 FRAT1 DVL3 0.029 WNT11 EP300
Cellular roles of Anthrax toxin 5.90E-05 0.008 MAP 2 K7 MAP 2 K1 0.001 MAPK3 TNF 0.061 MAP 2 K4 MAPK1
Methionine and Cysteine metabolism 6.62E-05 0.556 MTR MTR 0.001 LDHA AHCY 0.001 GOT2 LDHB
mRNA splicing 6.65E-05 0.040 PRPF3 SNRPA 0.007 PRPF3 PRPF3 0.002 PRPF3 SNRPA
Integrin signaling pathway 6.94E-05 0.006 ARF6 ILK 0.001 ITGAX ITGB7 0.098 RHOA RHOA
Validated nuclear estrogen receptor alpha network 7.38E-05 0.158 SET XBP1 0.004 LCOR HDAC1 0.001 DDX17 XBP1
Wnt signaling pathway 7.87E-05 0.010 SRCAP HDAC3 0.001 PRKCD CSNK2A2 0.068 GNB1 PPP2R5C
Arf6 signaling events 0.00010 0.116 EGFR GNA14 0.002 ACAP2 CYTH3 0.004 GNAQ NCK1
Alpha4 beta1 integrin signaling events 0.00012 0.095 ARF6 CD14 0.006 CDC42 CD14 0.002 YWHAZ ITGA4
FGF signaling pathway 0.00012 0.009 ETS2 ETS2 0.004 SPI1 PLCG1 0.032 MAPK1 MAPK1
Syndecan-4-mediated signaling events 0.00012 0.003 THBS1 CCL5 0.055 CXCR4 GIPC1 0.007 ACTN1 RHOA
AP-1 transcription factor network 0.00017 0.003 HLA-A ETS1 0.009 MMP9 TRIP6 0.063 CREB1 CDKN1B
Signaling events mediated by focal adhesion kinase 0.00021 0.009 ACTN4 RAP1B 0.001 ROCK2 ARHGEF7 0.233 RHOA RHOA
a6b1 and a6b4 Integrin signaling 0.00030 0.002 YWHAZ YWHAG 0.005 AKT1 PIK3R1 0.319 PIK3R1 YWHAQ
ATM pathway 0.00059 0.003 ATM ABL1 0.005 TOP3A ATM 0.472 TRIM28 SMC1A
Validated targets of C-MYC transcriptional repression 0.00062 0.009 CDKN1B CEBPD 0.001 CREB1 HDAC1 0.833 ALDH9A1 EP300
Apoptosis signaling pathway 0.00063 0.005 TNFRSF1A ATF4 0.002 BIRC3 LTB 0.767 PIK3CA HSPA5
Angiogenesis 0.00065 0.010 MAPKAPK2 CRKL 0.005 PRKCD GRAP 0.161 GSK3B RHOA
Cadherin signaling pathway 0.00072 0.009 CSNK2A2 FZD5 0.006 ACTA2 LEF1 0.167 WNT11 EGFR