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

Yu, Hui; Chen, Danqian; Oyebamiji, Olufunmilola; Zhao, Ying-Yong; Guo, Yan

doi:10.1186/s12920-020-00772-3

BMC Medical Genomics

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
Pathway	Aggregated p	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

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ISSN: 1755-8794

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