Disease table of WAARDENBURG SYNDROME OMIM ID: PS193500

Gene-disease associations table

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Gene	Associated with WAARDENBURG SYNDROME in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
EDN3	ClinVar, OMIM, HUMSAVAR	HGNC link	20q13.32	3	PS193500, PS142623, 209880
EDNRB	ClinVar, OMIM, HUMSAVAR	HGNC link	13q22.3	3	PS193500, 600501, PS142623
MITF	ClinVar, OMIM, HUMSAVAR	HGNC link	3p13	3	103500, PS155600, PS193500
PAX3	ClinVar, OMIM, HUMSAVAR	HGNC link	2q36.1	4	268220, PS193500, 142340, 122880
SNAI2	OMIM	HGNC link	8q11.21	2	PS193500, 172800
SOX10	ClinVar, OMIM, HUMSAVAR	HGNC link	22q13.1	2	PS193500, 609136
TYR	OMIM	HGNC link	11q14.3	4	PS193500, PS227220, PS155600, PS203100

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Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

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
SOX10	YES	11	COL11A2, GJB1, GJC2, NES, PMP22, EDNRB, MBP, MIA, MITF, MPZ, RET	2	EDNRB, MITF
SNAI2	YES	21	PTN, JAG1, L1CAM, CDH2, MMP2, MET, CXCL12, CXCR4, MMP9, FZD1, CDH1, VDR, CD44, CXADR, UBE2D3, LPAR2, CTGF, NETO2, HPGD, MMP17, POU5F1	0
PAX3	YES	6	BCL2L1, DPYSL2, MET, CXCR4, MITF, SHH	1	MITF
MITF	YES	27	BEST1, MET, MC1R, TYR, BCL2A1, TRAP, FOS, DCT, BIRC7, TRPM1, CD82, ITGA4, PPARGC1A, KIT, GPNMB, MLANA, KCNMA1, OCA2, PMEL, HOXB4, CDK2, PRKCB, TYRP1, CTSK, HIF1A, ACP5, SERPINF1	1	TYR
POU3F2	NO	8	FABP7, FOXP2, NKX2-1, PDE5A, DDC, GNRH1, PAX3, MITF	2	PAX3, MITF
SOX9	NO	25	SF1, AR, COL11A2, RET, RXFP2, NR5A1, CDK4, BEST1, DCT, TYR, COL2A1, KLF4, MIA, DCC, PRAME, SOX10, CDKN1A, NES, HES1, CEACAM1, MITF, AMH, SHH, POU3F2, ETV2	3	TYR, MITF, SOX10
CREB1	NO	90	NDC80, NRF1, IFNG, NR2F1, CYP19A1, CASP8, LDHA, SMAD6, SLC19A1, GSK3A, IL10, PSEN1, PPP2R2B, JUN, HPGD, IL2, GABPA, MC2R, CRTC1, AR, FLT1, SLC39A1, BDKRB2, NPY, PTGS2, MSMB, CFTR, HMOX1, MITF, AQP3, MUC5AC, STMN1, TRH, PCSK1, MMP2, CYP17A1, NOLC1, PRL, NMNAT2, TLR9, NTS, PLAT, FOS, BCL2L11, MUC4, GSK3B, CYP11B1, PPM1D, CCK, ETV3, PTGES, UXT, HLA-DOB, CGA, XPC, ACACA, SLC22A8, TH, VIP, BDKRB1, CYP11B2, POLD2, LAPTM4B, SOX9, PLAU, SNAI1, PPP2CA, SNAI2, SPRY2, HLA-DQB1, CCL5, CXCR4, ADRA1A, NR5A2, ERBB2, GRPR, BDNF, NR4A3, IL5RA, SLC20A1, RRM2B, LYL1, BCL2, CD4, NR2F6, NF1, IL6, CYP11A1, ODC1, FOXA1	2	SNAI2, MITF
LEF1	NO	32	AR, OCA2, PRL, NT5E, DLL1, CD1D, NCAM1, MMP7, CCL7, CEBPA, CCND1, CHGA, TCF3, CTNNB1, ALX4, BIRC5, RAG2, CLDN2, NRCAM, SPP1, MITF, IL13, SNAI2, EDA, IL4, DSG4, IL5, ELANE, ESR1, CTLA4, MYC, MYCBP	2	SNAI2, MITF

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regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
SOX10	YES	1	SOX9	0
SNAI2	YES	14	WT1, NCOR1, LEF1, RUNX2, TCF7, HDAC1, MTA1, HDAC2, TCF7L2, CREB1, EZH2, PER2, POU2F1, ESRRA	0
PAX3	YES	3	POU3F2, STAT3, TEAD1	0
MITF	YES	14	FOXD3, LEF1, SOX9, TCF4, POU3F2, ATF1, TRRAP, CREB1, ONECUT2, ONECUT1, PIAS3, PAX3, ZNF382, SOX10	2	PAX3, SOX10
EDNRB	YES	3	SP1, HIF1A, SOX10	1	SOX10
TYR	YES	4	TFEB, OTX2, SOX9, MITF	1	MITF
CXCR4	NO	24	IRF2, BCL6, NRF1, SNAI2, CREB1, KLF5, USF2, HDAC3, DNMT1, FOXO1, ERG, VHL, CREB3, PAX3, RELA, NFKB1, ETS1, HIF1A, YY1, YBX1, KLF2, MYC, ZBTB16, USF1	2	SNAI2, PAX3
MET	NO	13	SP1, FOXP2, PAX3, SMAD7, TP53, SNAI2, HIF1A, MITF, SP3, YBX1, PAX5, PAX6, STAT1	3	SNAI2, PAX3, MITF

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
SOX10	PAX3	Yes	1	POU3F2
EDN3	EDNRB	Yes	0
SOX10	MITF	No	1	EPAS1
SNAI2	PAX3	No	1	HDAC1
SNAI2	MITF	No	2	APP, STUB1

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

Interactions from BIOGRID - genetic

Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
SOX10	PAX3	Yes	0

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

Interactions from STRING

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Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
PAX3	MITF	Yes	activation, binding	7	BCL2, BMP4, MET, POU3F2, FOXD3, DICER1, TBX2
MITF	EDN3	Yes	activation, binding	3	EDNRB, FOS, EDN1
MITF	EDNRB	Yes	expression, binding	3	MAPK14, EDN3, EDN1
EDN3	EDNRB	Yes	binding	122	P2RY6, GPR17, KISS1, AGT, XCL1, PTGFR, GPR65, GHSR, CYSLTR2, ANXA1, NTS, CYSLTR1, EDN1, NPS, GCGR, SAA1, NMUR1, XCR1, F2R, HCRT, LPAR6, FFAR1, GNRH2, GNA14, EDN2, F2RL3, GPR68, NMUR2, GRM1, GCG, QRFP, GNRH1, OXT, GRP, PTAFR, CASR, F2RL1, PROK2, TAC1, TAC3, GNRHR, OPN4, FFAR3, NPFF, NPFFR2, P2RY1, F2RL2, FFAR2, PROK1, MITF, XCL2, TRH, GPR132, TACR1, ADRA1B, QRFPR, HCRTR2, P2RY10, HRH1, GPRC6A, EDNRA, GNG2, FPR2, TBXA2R, MLNR, CCKBR, LPAR3, APP, GNA15, NMBR, UTS2R, LPAR1, CCK, BDKRB2, MCHR2, NMB, AGTR1, NTSR2, LPAR5, AVPR1A, HCRTR1, OXTR, GNAQ, MLN, TRHR, LTB4R, GNA11, GPR4, BDKRB1, CHRM5, P2RY2, AVP, LTB4R2, PMCH, PROKR1, GRM5, NPSR1, KNG1, CCKAR, KISS1R, NTSR1, TACR3, GNB1, NPFFR1, MTRNR2L2, CHRM1, HTR2B, TACR2, GRPR, NMU, CHRM3, PTGER1, PROKR2, UTS2D, LPAR4, NMS, ADRA1D, HTR2A, ADRA1A, MCHR1, LPAR2, UTS2
SNAI2	PAX3	No	-	4	NOG, DICER1, BMP4, RUNX2
SNAI2	MITF	No	-	7	KIT, BMP4, SOX9, LEF1, TP53, CTNNB1, DICER1
SNAI2	EDNRB	No	-	1	MMP9
PAX3	EDN3	No	-	1	MITF
PAX3	EDNRB	No	-	1	MITF

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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
Melanogenesis	hsa04916	5.97	3	EDNRB, TYR, MITF
Pathways in cancer	hsa05200	3.98	2	EDNRB, MITF

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Melanogenesis (hsa04916)	-	5.97	0.001	TYR, EDNRB, PAX3, MITF
Cellular community	NEW	3.57	0.028	SNAI2, EDNRB, PAX3, MITF, SOX10

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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
G alpha (q) signalling events	R-HSA-416476	5.42	2	EDNRB, EDN3
Peptide ligand-binding receptors	R-HSA-375276	5.41	2	EDNRB, EDN3
Class A/1 (Rhodopsin-like receptors)	R-HSA-373076	4.69	2	EDN3, EDNRB
Gastrin-CREB signalling pathway via PKC and MAPK	R-HSA-881907	4.26	2	EDNRB, EDN3
GPCR ligand binding	R-HSA-500792	4.19	2	EDNRB, EDN3
GPCR downstream signaling	R-HSA-388396	3.07	2	EDN3, EDNRB
Signaling by GPCR	R-HSA-372790	2.68	2	EDNRB, EDN3
Signal Transduction	R-HSA-162582	1.78	2	EDNRB, EDN3

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
G alpha (q) signalling events (R-HSA-416476)	-	5.42	0.047	EDN3, EDNRB
Peptide ligand-binding receptors (R-HSA-375276)	-	5.41	0.048	EDN3, EDNRB

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

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GO	IC	Number of genes with the same GO	Genes
transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding (GO:0003705)	5.23	2	SNAI2, SOX10
transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001227)	4.61	2	SNAI2, MITF
G-protein coupled receptor binding (GO:0001664)	4.18	2	EDN3, EDNRB
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0000982)	3.94	2	SNAI2, MITF
RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	3.88	2	MITF, SOX10
core promoter proximal region sequence-specific DNA binding (GO:0000987)	3.83	2	SOX10, MITF
core promoter proximal region DNA binding (GO:0001159)	3.82	2	MITF, SOX10
chromatin binding (GO:0003682)	3.64	2	SNAI2, SOX10
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	3.37	2	MITF, SOX10
RNA polymerase II regulatory region DNA binding (GO:0001012)	3.36	2	SOX10, MITF

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
HMG box domain binding (GO:0071837)	NEW	6.85	0.012	PAX3, SOX10
DNA binding, bending (GO:0008301)	NEW	6.74	0.018	PAX3, SOX10
RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)	NEW	5.58	0.002	EDNRB, PAX3, SOX10
enhancer sequence-specific DNA binding (GO:0001158)	NEW	5.36	0.004	EDNRB, PAX3, SOX10
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	-	5.23	0.0	MITF, SNAI2, PAX3, EDNRB, SOX10
enhancer binding (GO:0035326)	NEW	5.21	0.008	EDNRB, PAX3, SOX10
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	-	4.61	0.014	SNAI2, PAX3, SOX10
transcription corepressor activity (GO:0003714)	NEW	4.33	0.008	PAX3, SNAI2, MITF, SOX10
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)	-	3.94	0.0	PAX3, SNAI2, EDNRB, MITF, SOX10
RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	-	3.88	0.003	PAX3, EDNRB, MITF, SOX10

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

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GO	IC	Number of genes with the same GO	Genes
vein smooth muscle contraction (GO:0014826)	8.34	2	EDN3, EDNRB
enteric nervous system development (GO:0048484)	7.33	2	EDNRB, SOX10
vascular smooth muscle contraction (GO:0014829)	7.16	2	EDNRB, EDN3
phasic smooth muscle contraction (GO:0014821)	6.96	2	EDNRB, EDN3
melanocyte differentiation (GO:0030318)	6.73	4	EDNRB, EDN3, MITF, SOX10
pigment cell differentiation (GO:0050931)	6.64	4	EDNRB, EDN3, MITF, SOX10
peripheral nervous system development (GO:0007422)	6.47	2	EDNRB, SOX10
vasoconstriction (GO:0042310)	6.36	2	EDNRB, EDN3
pigmentation (GO:0043473)	5.9	4	TYR, SNAI2, EDNRB, MITF
smooth muscle contraction (GO:0006939)	5.9	2	EDN3, EDNRB

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
spinal cord motor neuron migration (GO:0097476)	NEW	8.34	0.006	SNAI2, SOX10
motor neuron migration (GO:0097475)	NEW	8.34	0.006	SNAI2, SOX10
vein smooth muscle contraction (GO:0014826)	-	8.34	0.001	EDN3, EDNRB
enteric nervous system development (GO:0048484)	-	7.33	0.049	EDNRB, SOX10
vascular smooth muscle contraction (GO:0014829)	-	7.16	0.049	EDNRB, EDN3
melanin biosynthetic process (GO:0042438)	NEW	7.16	0.0	TYR, PAX3, MITF
melanin metabolic process (GO:0006582)	NEW	7.09	0.0	TYR, PAX3, MITF
developmental pigmentation (GO:0048066)	NEW	6.96	0.035	PAX3, MITF
phasic smooth muscle contraction (GO:0014821)	-	6.96	0.009	EDNRB, EDN3
astrocyte differentiation (GO:0048708)	NEW	6.78	0.038	PAX3, SOX10

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GO - cellular component annotation: shared terms / NET-GE enrichment

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GO	IC	Number of genes with the same GO	Genes
organelle membrane (GO:0031090)	1.97	2	EDNRB, TYR
nucleoplasm (GO:0005654)	1.89	3	PAX3, MITF, SOX10
cytosol (GO:0005829)	1.68	2	EDNRB, TYR
nuclear part (GO:0044428)	1.55	5	MITF, SNAI2, PAX3, EDNRB, SOX10
macromolecular complex (GO:0032991)	1.35	2	SNAI2, MITF
integral component of membrane (GO:0016021)	1.14	2	EDNRB, TYR
intrinsic component of membrane (GO:0031224)	1.13	2	EDNRB, TYR
nucleus (GO:0005634)	1.07	5	TYR, SNAI2, PAX3, SOX10, MITF
cytoplasm (GO:0005737)	1.01	3	SNAI2, TYR, SOX10
membrane part (GO:0044425)	0.95	3	EDNRB, TYR, SOX10

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
melanosome membrane (GO:0033162)	NEW	7.61	0.0	TYR, PAX3, MITF
protein-DNA complex (GO:0032993)	NEW	5.03	0.026	PAX3, MITF, SOX10
extracellular space (GO:0005615)	NEW	2.63	0.032	EDNRB, EDN3, PAX3, SNAI2, MITF, SOX10
extracellular region (GO:0005576)	NEW	2.18	0.046	EDNRB, EDN3, PAX3, SNAI2, MITF, SOX10

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