Disease table of OROFACIAL CLEFT OMIM ID: PS119530

Gene-disease associations table

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Gene	Associated with OROFACIAL CLEFT in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
BMP4	ClinVar, OMIM, HUMSAVAR	HGNC link	14q22.2	2	PS309800, PS119530
IRF6	OMIM, HUMSAVAR	HGNC link	1q32.2	3	PS119530, 119300, 119500
MSX1	ClinVar, OMIM, HUMSAVAR	HGNC link	4p16.2	3	PS106600, PS305100, PS119530
NECTIN1	ClinVar, OMIM	HGNC link	11q23.3	1	PS119530
SUMO1	OMIM	HGNC link	2q33.1	1	PS119530
TP63	ClinVar, OMIM, HUMSAVAR	HGNC link	3q28	6	106260, 103285, 604292, PS119530, PS183600, 603543

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Download the disease annotation in CSV format

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
TP63	YES	11	BAX, TCF4, VDR, KLF4, CDKN1A, FDXR, EVPL, SMARCD3, XPC, PPARA, DDB2	0
IRF6	YES	1	NR1H4	0
MSX1	YES	6	HEY1, DLK1, CGA, DKK1, NOTCH3, ZHX2	0
GATA4	NO	22	NKX2-5, FGF10, HDAC9, CYP17A1, NOS3, CCND2, BMP4, HESX1, HAMP, FCGR3B, STAR, ERBB2, FABP2, IAPP, NPPA, AMH, SUMO1, NPPB, IL5, SGPL1, FCGR2B, MEF2C	2	BMP4, SUMO1

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regulated gene	associated to this disease	# TFs	TFs
TP63	YES	3	SATB2, BRCA1, STAT3
BMP4	YES	4	POU5F1, FOXL1, ETS1, GATA4
SUMO1	YES	4	YBX1, STAT5A, BCL6, GATA4
MSX1	YES	2	PHOX2B, FOXE1

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
TP63	SUMO1	Yes	14	DAXX, TP63, SUMO1, FAS, PML, PSMD2, VCP, TP53, HNRNPK, MDM2, BRCA1, YAP1, HIPK2, UBE2I
IRF6	SUMO1	No	1	HHV8GK18_GP81

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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
TP63	IRF6	Yes	activation, binding	1	SERPINB5
BMP4	MSX1	Yes	activation, binding	11	LEF1, RUNX2, FGF4, FGF8, PAX3, WNT1, YBX1, BMP2, MYOD1, PAX9, WNT4
IRF6	MSX1	Yes	binding	1	CREBBP
TP63	BMP4	No	-	4	SHH, FGF8, CDKN1A, EGFR
TP63	SUMO1	No	-	6	MDM2, UBE2A, TP53, UBC, UBE2I, MDM4
TP63	MSX1	No	-	3	IRF6, FGF8, TP53
BMP4	IRF6	No	-	5	ATF2, JUN, ICAM1, EGR1, MSX1
BMP4	SUMO1	No	-	14	GATA4, PCNA, EGR1, CCND1, MAPK8, SMAD4, JUN, SMAD3, CDH1, MITF, NKX2-5, MYB, PAX6, KLF4
IRF6	SUMO1	No	-	11	CREBBP, NR3C1, ADAR, IRF1, IRF7, EGR1, JUN, SP100, ISG15, FOS, PML
SUMO1	MSX1	No	-	2	CREBBP, 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: NET-GE enrichment (no shared terms)

NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Herpes simplex infection (hsa05168)	NEW	5.08	0.011	IRF6, TP63, SUMO1, PVRL1
Infectious diseases: Viral	NEW	3.29	0.007	BMP4, SUMO1, IRF6, MSX1, TP63, PVRL1

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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
Interferon gamma signaling	R-HSA-877300	5.67	2	IRF6, SUMO1
Interferon Signaling	R-HSA-913531	4.95	2	IRF6, SUMO1
Cytokine Signaling in Immune system	R-HSA-1280215	3.74	2	IRF6, SUMO1
Immune System	R-HSA-168256	2.37	2	IRF6, SUMO1

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Phase 1 - Functionalization of compounds (R-HSA-211945)	NEW	6.7	0.019	IRF6, BMP4, SUMO1

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
p53 binding (GO:0002039)	5.53	2	MSX1, TP63
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228)	3.98	2	TP63, MSX1
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0000982)	3.94	2	TP63, MSX1
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981)	3.29	2	TP63, MSX1
protein homodimerization activity (GO:0042803)	3.16	2	NECTIN1, BMP4
double-stranded DNA binding (GO:0003690)	3.09	2	MSX1, TP63
regulatory region nucleic acid binding (GO:0001067)	3.03	3	IRF6, MSX1, TP63
regulatory region DNA binding (GO:0000975)	3.03	3	IRF6, TP63, MSX1
transcription regulatory region DNA binding (GO:0044212)	3.03	2	MSX1, TP63
sequence-specific DNA binding (GO:0043565)	2.79	2	TP63, MSX1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
activating transcription factor binding (GO:0033613)	NEW	5.68	0.001	BMP4, MSX1, SUMO1
p53 binding (GO:0002039)	-	5.53	0.01	MSX1, TP63, SUMO1
RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)	NEW	4.84	0.029	BMP4, MSX1, SUMO1
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	NEW	4.61	0.0	BMP4, MSX1, SUMO1, TP63
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	-	3.98	0.007	BMP4, MSX1, SUMO1, TP63
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)	-	3.94	0.007	BMP4, MSX1, SUMO1, TP63
sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	-	3.29	0.002	TP63, BMP4, MSX1, SUMO1, IRF6
transcription regulatory region DNA binding (GO:0044212)	-	3.03	0.005	MSX1, BMP4, TP63, SUMO1, IRF6
regulatory region nucleic acid binding (GO:0001067)	-	3.03	0.005	MSX1, BMP4, TP63, SUMO1, IRF6
regulatory region DNA binding (GO:0000975)	-	3.03	0.005	TP63, BMP4, MSX1, SUMO1, IRF6

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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
cloacal septation (GO:0060197)	8.63	2	BMP4, TP63
keratinocyte proliferation (GO:0043616)	7.24	2	IRF6, TP63
mesenchymal cell proliferation (GO:0010463)	7.16	2	BMP4, MSX1
smooth muscle tissue development (GO:0048745)	7.02	2	BMP4, TP63
camera-type eye morphogenesis (GO:0048593)	6.78	2	NECTIN1, BMP4
organ formation (GO:0048645)	6.73	2	BMP4, TP63
prostate gland epithelium morphogenesis (GO:0060740)	6.73	2	BMP4, TP63
regulation of odontogenesis (GO:0042481)	6.55	2	BMP4, MSX1
positive regulation of calcium ion transmembrane transporter activity (GO:1901021)	6.36	2	BMP4, SUMO1
embryonic hindlimb morphogenesis (GO:0035116)	6.36	2	BMP4, MSX1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
BMP signaling pathway involved in heart development (GO:0061312)	NEW	9.04	0.001	BMP4, MSX1
cloacal septation (GO:0060197)	-	8.63	0.0	BMP4, TP63
forebrain anterior/posterior pattern specification (GO:0021797)	NEW	7.94	0.017	MSX1, SUMO1
negative regulation of mesoderm development (GO:2000381)	NEW	7.78	0.002	BMP4, TP63
regulation of transcription from RNA polymerase II promoter involved in heart development (GO:1901213)	NEW	7.43	0.006	BMP4, MSX1
mammary gland epithelium development (GO:0061180)	NEW	7.43	0.023	BMP4, MSX1
keratinocyte proliferation (GO:0043616)	-	7.24	0.0	IRF6, BMP4, TP63
mesenchymal cell proliferation (GO:0010463)	-	7.16	0.034	BMP4, MSX1
smooth muscle tissue development (GO:0048745)	-	7.02	0.008	BMP4, TP63
cell surface receptor signaling pathway involved in heart development (GO:0061311)	NEW	6.96	0.016	BMP4, MSX1

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

Shared terms

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GO	IC	Number of genes with the same GO	Genes
chromatin (GO:0000785)	3.99	2	TP63, SUMO1
dendrite (GO:0030425)	3.92	2	TP63, SUMO1
synapse (GO:0045202)	3.58	2	NECTIN1, SUMO1
plasma membrane protein complex (GO:0098797)	3.55	2	NECTIN1, SUMO1
chromosomal part (GO:0044427)	3.18	2	TP63, SUMO1
neuron projection (GO:0043005)	3.12	3	NECTIN1, TP63, SUMO1
membrane protein complex (GO:0098796)	2.84	2	NECTIN1, SUMO1
neuron part (GO:0097458)	2.64	3	NECTIN1, TP63, SUMO1
cell projection (GO:0042995)	2.47	3	NECTIN1, TP63, SUMO1
extracellular region (GO:0005576)	2.18	2	NECTIN1, BMP4

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
nuclear chromatin (GO:0000790)	NEW	4.42	0.001	IRF6, MSX1, SUMO1, TP63
transcription factor complex (GO:0005667)	NEW	4.1	0.011	BMP4, MSX1, SUMO1, TP63
chromatin (GO:0000785)	-	3.99	0.0	TP63, BMP4, MSX1, SUMO1, IRF6
extracellular matrix (GO:0031012)	NEW	3.81	0.014	BMP4, TP63, SUMO1, IRF6
nuclear chromosome part (GO:0044454)	NEW	3.67	0.011	IRF6, MSX1, SUMO1, TP63
anchoring junction (GO:0070161)	NEW	3.61	0.043	BMP4, PVRL1, SUMO1, TP63
chromosomal part (GO:0044427)	-	3.18	0.005	MSX1, BMP4, TP63, SUMO1, IRF6
neuron projection (GO:0043005)	-	3.12	0.033	PVRL1, SUMO1, TP63
organelle lumen (GO:0043233)	NEW	3.05	0.015	MSX1, BMP4, TP63, SUMO1, IRF6
membrane-enclosed lumen (GO:0031974)	NEW	3.05	0.022	MSX1, BMP4, TP63, SUMO1, IRF6

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