Table 4.

Significantly altered pathways in cyst epithelia by Reactome (genes with VAF≥0.2)

Pathway Identifier	Pathway Name	Entities Founda	Entities Totala	Entities P Value	Submitted Entities Found
R-HSA-390471	Association of TriC/CCT with target proteins during biosynthesis	4	40	0.004	USP11;KIF13A;TCP1;CCT4
R-HSA-5620920	Cargo trafficking to the periciliary membrane	4	55	0.01	TCP1;PKD2;PKD1;CCT4
R-HSA-5617833	Cilium Assembly	8	207	0.02	DYNC2H1;CEP164;TCP1;CEP97;PKD2;KIF17;PKD1;CCT4
R-HSA-1852241	Organelle biogenesis and maintenance	11	334	0.02	DYNC2H1;NCOR1;CEP164;TCP1;TFAM;CEP97;PKD2;KIF17;PKD1;CCT4
R-HSA-390450	Folding of actin by CCT/TriC	2	13	0.02	TCP1;CCT4
R-HSA-4839726	Chromatin organization	9	257	0.02	KDM6B;NCOR1;TRRAP;DNMT3A;EP400;ELP3;PADI4;ARID1A;SMARCA2
R-HSA-3247509	Chromatin modifying enzymes	9	257	0.02	KDM6B;NCOR1;TRRAP;DNMT3A;EP400;ELP3;PADI4;ARID1A;SMARCA2
R-HSA-5576892	Phase 0 – rapid depolarization	3	47	0.04	CACNA2D1;SCN4A
R-HSA-163282	Mitochondrial transcription initiation	1	3	0.05	TFAM
R-HSA-4085023	Defective GFPT1 causes CMSTA1	1	3	0.05	GFPT1
R-HSA-73780	RNA polymerase III chain elongation	2	22	0.05	CRCP;POLR3E
R-HSA-2408550	Metabolism of ingested H2SeO4 and H2SeO3 into H2Se	2	22	0.05	GSR;PAPSS2
R-HSA-1655829	Regulation of cholesterol biosynthesis by SREBP (SREBF)	4	86	0.05	INSIG2;SC5D;SEC24D
R-HSA-73980	RNA polymerase III transcription termination	2	23	0.05	CRCP;POLR3E
R-HSA-3214858	RMTs methylate histone arginines	3	53	0.05	DNMT3A;ARID1A;SMARCA2
R-HSA-5620922	BBSome-mediated cargo-targeting to cilium	2	24	0.06	TCP1;CCT4
R-HSA-5620916	VxPx cargo-targeting to cilium	2	25	0.06	PKD2;PKD1

Pathway analysis was performed by Reactome (https://reactome.org/).

^aEntities, proteins with an accession sequence in UniPort and Ensemble databases.