A Proteomic Network Approach across the Kidney Stone Disease Reveals Endoplasmic Reticulum Stress and Crystal-Cell Interaction in the Kidney

Table 1

Gene Ontology analysis for the backbone network of a kidney stone.

Term	Count	%	value	Benjamini	FDR	Genes
GOTERM_BP_DIRECT
GO:0022617~extracellular matrix disassembly	5	16.129		0.00493	0.012443	BSG, A2M, MMP9, CDH1, FN1
GO:0006457~protein folding	6	19.3548		0.00388	0.019533	HSP90AB1, P4HB, HSP90B1, HSP90AA1, APCS, CALR
GO:0050821~protein stabilization	5	16.129		0.01573	0.119559	HSP90AB1, HSP90AA1, APOA1, CALR, GAPDH
GO:0036500~ATF6-mediated unfolded protein response	3	9.67742		0.01495	0.151433	HSP90B1, HSPA5, CALR
GO:0006950~response to stress	4	12.9032		0.01897	0.240659	HSP90AB1, MAPK1, HSP90B1, HSP90AA1
GO:0006898~receptor-mediated endocytosis	5	16.129		0.01786	0.271641	HSP90B1, HSP90AA1, APOA1, CALR, CD14
GO:0034975~protein folding in endoplasmic reticulum	3	9.67742		0.01839	0.326434	HSP90B1, HSPA5, CALR
GO:1900034~regulation of cellular response to heat	4	12.9032		0.02084	0.422888	HSP90AB1, MAPK1, HSP90AA1, YWHAE
GOTERM_CC_DIRECT
GO:0070062~extracellular exosome	24	77.4194				HSP90AB1, P4HB, A2M, BSG, APCS, HSP90AA1, MMP9, YWHAB, CDH1, ITGB2, CALR, YWHAE, PCK1, JUP, MAPK1, HSP90B1, APOA1, EIF4A1, YWHAQ, HSPA5, EGF, GAPDH, CD14, FN1
GO:0042470~melanosome	8	25.8065				HSP90AB1, P4HB, HSP90B1, BSG, HSP90AA1, YWHAB, HSPA5, YWHAE
GO:0005925~focal adhesion	11	35.4839				JUP, MAPK1, P4HB, HSP90B1, BSG, YWHAB, YWHAQ, CDH1, HSPA5, CALR, YWHAE
GO:0031012~extracellular matrix	10	32.2581				JUP, P4HB, HSP90B1, HSP90AA1, APCS, EIF4A1, HSPA5, CALR, GAPDH, FN1
GO:0071682~endocytic vesicle lumen	4	12.9032			0.002338	HSP90B1, HSP90AA1, APOA1, CALR
GO:0005829~cytosol	18	58.0645			0.002354	HSP90AB1, AR, A2M, HSP90AA1, EXOC7, YWHAB, CALR, TAB1, YWHAE, PCK1, JUP, MAPK1, HSP90B1, APOA1, EIF4A1, YWHAQ, HBG2, GAPDH
GO:0005576~extracellular region	13	41.9355			0.003128	P4HB, A2M, BMP2, APCS, HSP90AA1, MMP9, CDH1, CALR, HSP90B1, APOA1, EGF, CD14, FN1
GO:0005913~cell-cell adherens junction	7	22.5807			0.011684	HSP90AB1, JUP, BSG, YWHAB, CDH1, HSPA5, YWHAE
GO:0016020~membrane	14	45.1613			0.013736	HSP90AB1, HSP90B1, BSG, HSP90AA1, EXOC7, EIF4A1, YWHAB, YWHAQ, CDH1, ITGB2, HSPA5, CALR, GAPDH, YWHAE
GO:0072562~blood microparticle	5	16.129		0.00102	0.091484	A2M, APOA1, APCS, HBG2, FN1
GO:0034663~endoplasmic reticulum chaperone complex	3	9.67742		0.00158	0.155484	P4HB, HSP90B1, HSPA5
GO:0009986~cell surface	7	22.5807		0.00232	0.249403	HSP90AB1, BMP2, HSP90AA1, APOA1, ITGB2, HSPA5, CALR
GO:0005788~endoplasmic reticulum lumen	5	16.129		0.00232	0.269618	P4HB, HSP90B1, APOA1, HSPA5, CALR
GOTERM_MF_DIRECT
GO:0005515~protein binding	27	87.0968				HSP90AB1, A2M, EXOC7, MMP9, ITGB2, CDH1, CALR, APOA1, HSPA5, EGF, GAPDH, FN1, P4HB, AR, BSG, BMP2, CTBP2, HSP90AA1, YWHAB, TAB1, YWHAE, JUP, MAPK1, HSP90B1, EIF4A1, YWHAQ, CD14
GO:0001948~glycoprotein binding	6	19.3548				HSP90AB1, HSP90AA1, CDH1, ITGB2, HSPA5, CALR
GO:0051082~unfolded protein binding	6	19.3548			0.001626	HSP90AB1, HSP90B1, HSP90AA1, APCS, HSPA5, CALR
GO:0098641~cadherin binding involved in cell-cell adhesion	7	22.5807			0.015318	HSP90AB1, JUP, BSG, YWHAB, CDH1, HSPA5, YWHAE
GO:0019899~enzyme binding	7	22.5807			0.032354	P4HB, AR, A2M, APOA1, YWHAB, HSPA5, YWHAE
GO:0023026~MHC class II protein complex binding	3	9.67742		0.01158	0.47498	HSP90AB1, HSP90AA1, YWHAE
KEGG_PATHWAY
hsa05200: pathways in cancer	12	38.7097				HSP90AB1, JUP, MAPK1, AR, HSP90B1, BMP2, HSP90AA1, CTBP2, MMP9, CDH1, EGF, FN1
hsa04151: PI3K-Akt signaling pathway	10	32.2581			0.004295	HSP90AB1, MAPK1, HSP90B1, HSP90AA1, YWHAB, YWHAQ, EGF, YWHAE, FN1, PCK1
hsa05215: prostate cancer	6	19.3548			0.022701	HSP90AB1, MAPK1, AR, HSP90B1, HSP90AA1, EGF
hsa04114: oocyte meiosis	6	19.3548		0.00185	0.063994	MAPK1, AR, YWHAB, YWHAQ, PPP3R2, YWHAE
hsa04621: NOD-like receptor signaling pathway	5	16.129		0.0015	0.064592	HSP90AB1, MAPK1, HSP90B1, HSP90AA1, TAB1
hsa04390: Hippo signaling pathway	6	19.3548		0.00577	0.299238	BMP2, YWHAB, YWHAQ, CDH1, ITGB2, YWHAE
hsa04141: protein processing in endoplasmic reticulum	6	19.3548		0.00833	0.503915	HSP90AB1, P4HB, HSP90B1, HSP90AA1, HSPA5, CALR
hsa05219: bladder cancer	4	12.9032		0.0087	0.601459	MAPK1, MMP9, CDH1, EGF
hsa04915: estrogen signaling pathway	5	16.129		0.00813	0.632287	HSP90AB1, MAPK1, HSP90B1, HSP90AA1, MMP9