Disease table of RENAL CELL CARCINOMA, NONPAPILLARY OMIM ID: 144700

Gene-disease associations table

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Gene	Associated with RENAL CELL CARCINOMA, NONPAPILLARY in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
DIRC2	OMIM	HGNC link	3q21.1	1	144700
FLCN	OMIM, HUMSAVAR	HGNC link	17p11.2	4	135150, 144700, 173600, 114500
HNF1A	OMIM	HGNC link	12q24.31	6	125853, 222100, 144700, 142330, 612520, 600496
HNF1B	OMIM	HGNC link	17q12	3	125853, 137920, 144700
OGG1	OMIM	HGNC link	3p25.3	1	144700
RNF139	OMIM	HGNC link	8q24.13	1	144700
VHL	OMIM, HUMSAVAR	HGNC link	3p25.3	4	193300, 144700, PS133100, 171300

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Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By sub-band

Shared sub_band	Number of genes associated with the disease	Genes associated with the disease
3p25.3	2	OGG1, VHL

By band

Shared band	Number of genes associated with the disease	Genes associated with the disease
3p25	2	OGG1, VHL

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
3p2	2	OGG1, VHL

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
3p	2	OGG1, VHL

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
3	3	OGG1, DIRC2, VHL
17	2	FLCN, HNF1B

Transcription Factors (TF) annotation from TRRUST

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TF	associated to this disease	# regulated genes	Regulated genes	# regulated genes associated with this disease	Regulated genes associated with this disease
VHL	YES	18	CA9, STRA13, TCF4, TFRC, ANGPT2, CXCR4, CCND1, DAB2, KLF10, CDKN1C, CA12, TP53, NMU, HIF1A, SPARC, VEGFA, IGF1R, CDKN1B	0
HNF1A	YES	26	GPR39, FABP1, CYP1A2, NT5E, SLC22A9, ALB, SLCO1B3, UGT2B7, UGT2B17, SLC22A10, APOM, CDH17, IGFBP1, TM4SF1, CRP, UGT1A1, UGT1A8, LCT, UGT1A7, AKR1C4, UGT1A10, ACAT2, UGT1A9, AFP, CSRP1, MTTP	0

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regulated gene	associated to this disease	# TFs	TFs
VHL	YES	1	HIF1A
HNF1A	YES	2	RXRA, HNF4A
OGG1	YES	2	NFYA, TP53

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
HNF1B	HNF1A	Yes	2	HNF1A, PCBD1
FLCN	VHL	No	2	GAG-POL, APP
VHL	HNF1A	No	5	KAT2B, ACTB, EP300, CBX3, SIRT1

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic

Interactions from STRING

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Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
FLCN	VHL	No	-	1	CCND1
FLCN	HNF1A	No	-	1	CCND1
HNF1B	HNF1A	No	-	4	ONECUT1, PCBD1, CREBBP, DPP4
VHL	HNF1A	No	-	4	MYC, HDAC1, EP300, CCND1
VHL	RNF139	No	-	2	UBC, COPS5
VHL	OGG1	No	-	1	TP53

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CORUM

Interactions from CENSUS

Interactions from PDB

Interactions from manually curated literature

KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

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KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Maturity onset diabetes of the young	hsa04950	8.07	2	HNF1B, HNF1A
Renal cell carcinoma	hsa05211	6.6	2	VHL, FLCN

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Maturity onset diabetes of the young (hsa04950)	-	8.07	0.003	HNF1B, HNF1A
Renal cell carcinoma (hsa05211)	-	6.6	0.02	VHL, FLCN

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REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

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REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Regulation of beta-cell development	R-HSA-186712	7.98	2	HNF1B, HNF1A
Developmental Biology	R-HSA-1266738	3.48	2	HNF1B, HNF1A

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Regulation of beta-cell development (R-HSA-186712)	-	7.98	0.002	HNF1B, HNF1A

GO - molecular function annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
ubiquitin protein ligase activity (GO:0061630)	4.47	2	VHL, RNF139
ubiquitin-like protein ligase activity (GO:0061659)	4.44	2	VHL, RNF139
ubiquitin-protein transferase activity (GO:0004842)	3.73	2	VHL, RNF139
ubiquitin-like protein transferase activity (GO:0019787)	3.69	2	VHL, RNF139
protein heterodimerization activity (GO:0046982)	3.64	2	HNF1B, HNF1A
transcription factor binding (GO:0008134)	3.46	2	VHL, HNF1A
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981)	3.29	2	HNF1B, HNF1A
protein homodimerization activity (GO:0042803)	3.16	2	HNF1B, HNF1A
protein complex binding (GO:0032403)	3.09	2	HNF1B, FLCN
transcription regulatory region DNA binding (GO:0044212)	3.03	2	HNF1B, HNF1A

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
protein complex binding (GO:0032403)	-	3.09	0.001	VHL, HNF1A, OGG1, HNF1B, RNF139, FLCN

GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
regulation of pronephros size (GO:0035565)	9.04	2	HNF1B, HNF1A
regulation of kidney size (GO:0035564)	8.12	2	HNF1B, HNF1A
positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)	6.9	2	HNF1B, HNF1A
negative regulation of kidney development (GO:0090185)	6.9	2	HNF1B, FLCN
regulation of transcription initiation from RNA polymerase II promoter (GO:0060260)	6.59	2	HNF1B, HNF1A
positive regulation of DNA-templated transcription, initiation (GO:2000144)	6.55	2	HNF1B, HNF1A
endocrine pancreas development (GO:0031018)	6.36	2	HNF1B, HNF1A
regulation of DNA-templated transcription, initiation (GO:2000142)	6.29	2	HNF1B, HNF1A
insulin secretion (GO:0030073)	6.09	2	HNF1B, HNF1A
regulation of kidney development (GO:0090183)	5.72	2	HNF1B, FLCN

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)	-	6.9	0.008	HNF1B, HNF1A
regulation of transcription initiation from RNA polymerase II promoter (GO:0060260)	-	6.59	0.045	HNF1B, HNF1A
positive regulation of DNA-templated transcription, initiation (GO:2000144)	-	6.55	0.002	HNF1B, HNF1A
regulation of DNA-templated transcription, initiation (GO:2000142)	-	6.29	0.008	HNF1B, HNF1A
insulin secretion (GO:0030073)	-	6.09	0.036	HNF1B, HNF1A
regulation of kidney development (GO:0090183)	-	5.72	0.01	VHL, HNF1B, FLCN

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GO - cellular component annotation: shared terms (no NET-GE enrichment)

Shared terms

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GO	IC	Number of genes with the same GO	Genes
primary cilium (GO:0072372)	4.64	2	HNF1A, FLCN
transcription factor complex (GO:0005667)	4.1	2	HNF1B, HNF1A
lytic vacuole (GO:0000323)	3.89	2	DIRC2, FLCN
lysosome (GO:0005764)	3.89	2	DIRC2, FLCN
cilium (GO:0005929)	3.89	2	HNF1A, FLCN
vacuole (GO:0005773)	2.92	2	DIRC2, FLCN
endoplasmic reticulum (GO:0005783)	2.56	2	VHL, RNF139
cell projection (GO:0042995)	2.47	2	HNF1A, FLCN
mitochondrion (GO:0005739)	2.42	2	VHL, OGG1
nucleoplasm (GO:0005654)	1.89	4	VHL, HNF1B, HNF1A, OGG1

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