Disease table of TOOTH AGENESIS, SELECTIVE OMIM ID: PS106600

Gene-disease associations table

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Gene	Associated with TOOTH AGENESIS, SELECTIVE in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
EDA	ClinVar, OMIM, HUMSAVAR	HGNC link	Xq13.1	2	PS106600, PS305100
LRP6	ClinVar, OMIM	HGNC link	12p13.2	2	PS106600, 610947
MSX1	ClinVar, OMIM, HUMSAVAR	HGNC link	4p16.2	3	PS106600, PS305100, PS119530
PAX9	ClinVar, OMIM, HUMSAVAR	HGNC link	14q13.3	1	PS106600
WNT10A	ClinVar, OMIM, HUMSAVAR	HGNC link	2q35	3	PS106600, 224750, 257980

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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
MSX1	YES	6	HEY1, DLK1, CGA, DKK1, NOTCH3, ZHX2	0

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regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
MSX1	YES	2	PHOX2B, FOXE1	0
EDA	YES	1	LEF1	0

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Interactions from BIOGRID - physical

Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
MSX1	PAX9	No	1	TLE2
PAX9	WNT10A	No	1	EWSR1

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
MSX1	PAX9	Yes	binding	2	FGF8, BMP4
LRP6	WNT10A	Yes	activation, binding	28	WNT2B, WNT5A, FZD1, WNT10B, WNT8A, FZD2, WNT9A, WNT3A, WNT5B, WNT8B, FZD8, WNT3, WNT1, FZD4, FZD3, WNT16, WIF1, WNT11, FZD6, FZD5, FZD10, WNT2, FZD7, WNT9B, WNT6, WNT7A, WNT7B, WNT4
MSX1	LRP6	No	-	2	WNT1, WNT4
MSX1	WNT10A	No	-	2	WNT1, WNT4
EDA	LRP6	No	-	1	WNT6
EDA	WNT10A	No	-	1	WNT6

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

Interactions from CORUM

Gene1	Gene2	Direct Interaction	Complexes	Number of shared interactors	Shared genes in interaction
MSX1	PAX9	Yes	PAX9-MSX1 complex	0

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

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
Wnt signaling pathway	hsa04310	5.49	2	WNT10A, LRP6
HTLV-I infection	hsa05166	4.59	2	WNT10A, MSX1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Hedgehog signaling pathway (hsa04340)	NEW	7.01	0.0	EDA, WNT10A, LRP6
Basal cell carcinoma (hsa05217)	NEW	6.79	0.0	EDA, WNT10A, LRP6
Signaling pathways regulating pluripotency of stem cells (hsa04550)	NEW	5.6	0.013	EDA, WNT10A, LRP6
Wnt signaling pathway (hsa04310)	-	5.49	0.012	EDA, WNT10A, LRP6
HTLV-I infection (hsa05166)	-	4.59	0.005	EDA, WNT10A, MSX1, LRP6
Cancers: Specific types	NEW	4.1	0.014	EDA, WNT10A, MSX1, LRP6
Pathways in cancer (hsa05200)	NEW	3.98	0.023	EDA, WNT10A, LRP6, MSX1

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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
Signaling by Wnt	R-HSA-195721	4.79	2	WNT10A, LRP6
Signal Transduction	R-HSA-162582	1.78	2	WNT10A, LRP6

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Class B/2 (Secretin family receptors) (R-HSA-373080)	NEW	6.52	0.003	EDA, WNT10A, LRP6
Signaling by Wnt (R-HSA-195721)	-	4.79	0.007	EDA, WNT10A, PAX9, LRP6

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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
frizzled binding (GO:0005109)	6.1	2	WNT10A, LRP6
G-protein coupled receptor binding (GO:0001664)	4.18	2	WNT10A, LRP6
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228)	3.98	2	PAX9, MSX1
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	3.37	2	PAX9, MSX1
RNA polymerase II regulatory region DNA binding (GO:0001012)	3.36	2	PAX9, MSX1
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981)	3.29	2	PAX9, MSX1
transcription regulatory region sequence-specific DNA binding (GO:0000976)	3.24	2	PAX9, MSX1
sequence-specific double-stranded DNA binding (GO:1990837)	3.2	2	PAX9, MSX1
double-stranded DNA binding (GO:0003690)	3.09	2	PAX9, MSX1
transcription regulatory region DNA binding (GO:0044212)	3.03	2	PAX9, MSX1

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
frizzled binding (GO:0005109)	-	6.1	0.002	WNT10A, LRP6

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
neural crest cell differentiation (GO:0014033)	7.94	2	WNT10A, LRP6
cartilage morphogenesis (GO:0060536)	7.33	2	LRP6, MSX1
regulation of odontogenesis (GO:0042481)	6.55	3	WNT10A, MSX1, PAX9
mesenchymal cell differentiation (GO:0048762)	6.51	2	WNT10A, LRP6
face morphogenesis (GO:0060325)	6.29	3	LRP6, PAX9, MSX1
hair follicle development (GO:0001942)	6.02	2	EDA, WNT10A
skin development (GO:0043588)	5.84	2	EDA, WNT10A
epithelial to mesenchymal transition (GO:0001837)	5.76	2	LRP6, MSX1
molting cycle process (GO:0022404)	5.54	2	EDA, WNT10A
hair cycle process (GO:0022405)	5.54	2	EDA, WNT10A

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
neural crest cell differentiation (GO:0014033)	-	7.94	0.008	WNT10A, LRP6
cartilage morphogenesis (GO:0060536)	-	7.33	0.016	LRP6, MSX1
ectodermal placode formation (GO:0060788)	NEW	7.02	0.004	EDA, LRP6
cell surface receptor signaling pathway involved in heart development (GO:0061311)	NEW	6.96	0.047	LRP6, MSX1
regulation of odontogenesis (GO:0042481)	-	6.55	0.0	EDA, WNT10A, MSX1, PAX9
mesenchymal cell differentiation (GO:0048762)	-	6.51	0.009	WNT10A, LRP6
embryonic hindlimb morphogenesis (GO:0035116)	NEW	6.36	0.013	LRP6, MSX1
face morphogenesis (GO:0060325)	-	6.29	0.001	MSX1, PAX9, LRP6
embryonic forelimb morphogenesis (GO:0035115)	NEW	6.26	0.015	LRP6, MSX1
bone morphogenesis (GO:0060349)	NEW	6.2	0.011	LRP6, MSX1

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

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GO	IC	Number of genes with the same GO	Genes
extracellular region (GO:0005576)	2.18	3	EDA, WNT10A, LRP6
plasma membrane part (GO:0044459)	1.95	2	EDA, LRP6
protein complex (GO:0043234)	1.51	2	EDA, LRP6
plasma membrane (GO:0005886)	1.39	2	EDA, LRP6
macromolecular complex (GO:0032991)	1.35	2	EDA, LRP6
integral component of membrane (GO:0016021)	1.14	2	EDA, LRP6
intrinsic component of membrane (GO:0031224)	1.13	2	EDA, LRP6
nucleus (GO:0005634)	1.07	2	PAX9, MSX1
membrane part (GO:0044425)	0.95	2	EDA, LRP6
cytoplasmic part (GO:0044444)	0.82	2	EDA, LRP6

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