Disease table of TOOTH AGENESIS, SELECTIVE OMIM ID: PS106600

Gene-disease associations table

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

Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

Transcription Factors (TF) annotation from TRRUST

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

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

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

Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
MSX1	LRP6	No	-	2	WNT1, WNT4
MSX1	PAX9	Yes	binding	2	FGF8, BMP4
MSX1	WNT10A	No	-	2	WNT1, WNT4
EDA	LRP6	No	-	1	WNT6
EDA	WNT10A	No	-	1	WNT6
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

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

KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
HTLV-I infection	hsa05166	4.59	2	WNT10A, MSX1
Wnt signaling pathway	hsa04310	5.49	2	WNT10A, LRP6

NET-GE enrichment

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

REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

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

NET-GE enrichment

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

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

Shared terms

GO	IC	Number of genes with the same GO	Genes
binding (GO:0005488)	0.18	5	EDA, MSX1, WNT10A, LRP6, PAX9
protein binding (GO:0005515)	0.46	5	EDA, MSX1, WNT10A, PAX9, LRP6
receptor binding (GO:0005102)	2.43	3	EDA, WNT10A, LRP6
sequence-specific DNA binding (GO:0043565)	2.79	2	PAX9, MSX1
sequence-specific double-stranded DNA binding (GO:1990837)	3.2	2	PAX9, MSX1
transcription regulatory region DNA binding (GO:0044212)	3.03	2	PAX9, MSX1
transcription factor activity, sequence-specific DNA binding (GO:0003700)	2.65	2	PAX9, MSX1
regulatory region nucleic acid binding (GO:0001067)	3.03	2	PAX9, MSX1
regulatory region DNA binding (GO:0000975)	3.03	2	PAX9, MSX1
RNA polymerase II regulatory region DNA binding (GO:0001012)	3.36	2	PAX9, MSX1
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228)	3.98	2	PAX9, MSX1
frizzled binding (GO:0005109)	6.1	2	WNT10A, LRP6
transcription regulatory region sequence-specific DNA binding (GO:0000976)	3.24	2	PAX9, MSX1
nucleic acid binding transcription factor activity (GO:0001071)	2.65	2	PAX9, MSX1
nucleic acid binding (GO:0003676)	1.44	2	PAX9, MSX1
DNA binding (GO:0003677)	1.92	2	PAX9, MSX1
G-protein coupled receptor binding (GO:0001664)	4.18	2	WNT10A, LRP6
double-stranded DNA binding (GO:0003690)	3.09	2	PAX9, MSX1
organic cyclic compound binding (GO:0097159)	1.05	2	PAX9, MSX1
heterocyclic compound binding (GO:1901363)	1.06	2	PAX9, MSX1
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981)	3.29	2	PAX9, MSX1
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	3.37	2	PAX9, MSX1

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

GO	IC	Number of genes with the same GO	Genes
developmental process (GO:0032502)	1.36	5	EDA, WNT10A, LRP6, PAX9, MSX1
organ morphogenesis (GO:0009887)	3.55	5	EDA, MSX1, WNT10A, LRP6, PAX9
single-multicellular organism process (GO:0044707)	1.78	5	EDA, WNT10A, PAX9, LRP6, MSX1
positive regulation of metabolic process (GO:0009893)	1.74	5	EDA, MSX1, WNT10A, LRP6, PAX9
regulation of metabolic process (GO:0019222)	1.02	5	EDA, MSX1, WNT10A, LRP6, PAX9
odontogenesis (GO:0042476)	5.19	5	EDA, WNT10A, PAX9, LRP6, MSX1
regulation of macromolecule metabolic process (GO:0060255)	1.08	5	EDA, WNT10A, PAX9, LRP6, MSX1
regulation of gene expression (GO:0010468)	1.37	5	EDA, MSX1, WNT10A, LRP6, PAX9
multicellular organismal process (GO:0032501)	1.45	5	EDA, MSX1, WNT10A, PAX9, LRP6
anatomical structure development (GO:0048856)	1.58	5	EDA, MSX1, WNT10A, LRP6, PAX9
regulation of biological process (GO:0050789)	0.45	5	EDA, WNT10A, PAX9, LRP6, MSX1
single-organism developmental process (GO:0044767)	1.49	5	EDA, MSX1, WNT10A, LRP6, PAX9
positive regulation of gene expression (GO:0010628)	2.35	5	EDA, WNT10A, PAX9, LRP6, MSX1
biological regulation (GO:0065007)	0.39	5	EDA, MSX1, WNT10A, LRP6, PAX9
single-organism process (GO:0044699)	0.48	5	EDA, MSX1, WNT10A, LRP6, PAX9
positive regulation of biological process (GO:0048518)	1.2	5	EDA, MSX1, WNT10A, PAX9, LRP6
cellular process (GO:0009987)	0.26	5	EDA, WNT10A, PAX9, LRP6, MSX1
anatomical structure morphogenesis (GO:0009653)	2.53	5	EDA, MSX1, WNT10A, LRP6, PAX9
multicellular organism development (GO:0007275)	2.54	5	EDA, WNT10A, LRP6, PAX9, MSX1
regulation of cellular process (GO:0050794)	0.5	5	EDA, MSX1, WNT10A, LRP6, PAX9
positive regulation of macromolecule metabolic process (GO:0010604)	1.81	5	EDA, MSX1, WNT10A, LRP6, PAX9
regulation of primary metabolic process (GO:0080090)	1.08	4	EDA, MSX1, PAX9, LRP6
regulation of cellular biosynthetic process (GO:0031326)	1.38	4	EDA, PAX9, LRP6, MSX1
cell differentiation (GO:0030154)	2.14	4	EDA, WNT10A, MSX1, LRP6
regulation of cellular metabolic process (GO:0031323)	1.07	4	EDA, LRP6, PAX9, MSX1
signal transduction (GO:0007165)	1.28	4	EDA, WNT10A, MSX1, LRP6
cell surface receptor signaling pathway (GO:0007166)	2.09	4	EDA, WNT10A, MSX1, LRP6
cellular developmental process (GO:0048869)	1.82	4	EDA, WNT10A, MSX1, LRP6
regulation of cellular macromolecule biosynthetic process (GO:2000112)	1.46	4	EDA, LRP6, PAX9, MSX1
regulation of developmental process (GO:0050793)	2.1	4	WNT10A, PAX9, LRP6, MSX1
regulation of nucleobase-containing compound metabolic process (GO:0019219)	1.43	4	EDA, PAX9, LRP6, MSX1
regulation of biosynthetic process (GO:0009889)	1.37	4	EDA, LRP6, PAX9, MSX1
regulation of nucleic acid-templated transcription (GO:1903506)	1.55	4	EDA, MSX1, LRP6, PAX9
single-organism cellular process (GO:0044763)	0.65	4	EDA, WNT10A, MSX1, LRP6
regulation of nitrogen compound metabolic process (GO:0051171)	1.36	4	EDA, LRP6, PAX9, MSX1
regulation of multicellular organismal process (GO:0051239)	1.87	4	MSX1, WNT10A, PAX9, LRP6
regulation of RNA biosynthetic process (GO:2001141)	1.55	4	EDA, PAX9, LRP6, MSX1
response to stimulus (GO:0050896)	1.22	4	EDA, WNT10A, PAX9, LRP6
regulation of RNA metabolic process (GO:0051252)	1.52	4	EDA, PAX9, LRP6, MSX1
regulation of transcription, DNA-templated (GO:0006355)	1.56	4	EDA, LRP6, PAX9, MSX1
regulation of macromolecule biosynthetic process (GO:0010556)	1.43	4	EDA, MSX1, PAX9, LRP6
regulation of multicellular organismal development (GO:2000026)	2.31	4	MSX1, WNT10A, LRP6, PAX9
positive regulation of cellular process (GO:0048522)	1.3	4	EDA, PAX9, LRP6, MSX1
negative regulation of metabolic process (GO:0009892)	1.93	3	LRP6, PAX9, MSX1
positive regulation of biosynthetic process (GO:0009891)	2.29	3	LRP6, PAX9, MSX1
positive regulation of cellular metabolic process (GO:0031325)	1.81	3	LRP6, PAX9, MSX1
positive regulation of response to stimulus (GO:0048584)	2.18	3	EDA, LRP6, MSX1
regulation of response to stimulus (GO:0048583)	1.54	3	EDA, LRP6, MSX1
positive regulation of signaling (GO:0023056)	2.41	3	EDA, LRP6, MSX1
face morphogenesis (GO:0060325)	6.29	3	LRP6, PAX9, MSX1
cellular response to chemical stimulus (GO:0070887)	2.57	3	WNT10A, PAX9, LRP6
regulation of signaling (GO:0023051)	1.72	3	EDA, LRP6, MSX1
positive regulation of cell communication (GO:0010647)	2.41	3	EDA, LRP6, MSX1
regulation of cell communication (GO:0010646)	1.73	3	EDA, LRP6, MSX1
cellular response to stimulus (GO:0051716)	1.97	3	WNT10A, PAX9, LRP6
negative regulation of macromolecule metabolic process (GO:0010605)	2.01	3	LRP6, PAX9, MSX1
regulation of signal transduction (GO:0009966)	1.84	3	EDA, LRP6, MSX1
positive regulation of signal transduction (GO:0009967)	2.5	3	EDA, LRP6, MSX1
regulation of anatomical structure morphogenesis (GO:0022603)	2.79	3	WNT10A, PAX9, MSX1
organic substance metabolic process (GO:0071704)	0.63	3	EDA, PAX9, MSX1
cellular response to organic substance (GO:0071310)	2.78	3	WNT10A, PAX9, LRP6
animal organ development (GO:0048513)	2.53	3	EDA, WNT10A, MSX1
tissue morphogenesis (GO:0048729)	3.87	3	WNT10A, MSX1, LRP6
negative regulation of biological process (GO:0048519)	1.33	3	LRP6, PAX9, MSX1
regulation of molecular function (GO:0065009)	1.78	3	EDA, LRP6, MSX1
positive regulation of nucleic acid-templated transcription (GO:1903508)	2.56	3	PAX9, LRP6, MSX1
negative regulation of cellular metabolic process (GO:0031324)	2.01	3	MSX1, LRP6, PAX9
positive regulation of nucleobase-containing compound metabolic process (GO:0045935)	2.35	3	LRP6, PAX9, MSX1
tissue development (GO:0009888)	3.27	3	EDA, PAX9, MSX1
positive regulation of transcription, DNA-templated (GO:0045893)	2.56	3	LRP6, PAX9, MSX1
metabolic process (GO:0008152)	0.58	3	EDA, PAX9, MSX1
positive regulation of nitrogen compound metabolic process (GO:0051173)	2.29	3	LRP6, PAX9, MSX1
response to chemical (GO:0042221)	1.98	3	WNT10A, LRP6, PAX9
response to organic substance (GO:0010033)	2.2	3	WNT10A, LRP6, PAX9
positive regulation of cellular biosynthetic process (GO:0031328)	2.3	3	PAX9, LRP6, MSX1
odontogenesis of dentin-containing tooth (GO:0042475)	5.52	3	EDA, LRP6, MSX1
positive regulation of RNA metabolic process (GO:0051254)	2.51	3	PAX9, LRP6, MSX1
macromolecule metabolic process (GO:0043170)	0.83	3	EDA, PAX9, MSX1
positive regulation of RNA biosynthetic process (GO:1902680)	2.54	3	PAX9, LRP6, MSX1
positive regulation of macromolecule biosynthetic process (GO:0010557)	2.39	3	PAX9, LRP6, MSX1
regulation of transcription from RNA polymerase II promoter (GO:0006357)	2.24	3	PAX9, LRP6, MSX1
positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	2.81	3	PAX9, LRP6, MSX1
regulation of organ morphogenesis (GO:2000027)	4.22	3	WNT10A, MSX1, PAX9
regulation of odontogenesis (GO:0042481)	6.55	3	WNT10A, MSX1, PAX9
negative regulation of cellular process (GO:0048523)	1.41	3	PAX9, LRP6, MSX1
protein localization (GO:0008104)	2.36	2	LRP6, MSX1
regulation of Wnt signaling pathway (GO:0030111)	3.98	2	EDA, LRP6
organic cyclic compound biosynthetic process (GO:1901362)	1.66	2	PAX9, MSX1
cell surface receptor signaling pathway involved in cell-cell signaling (GO:1905114)	3.79	2	WNT10A, LRP6
organic cyclic compound metabolic process (GO:1901360)	1.26	2	PAX9, MSX1
neural crest cell differentiation (GO:0014033)	7.94	2	WNT10A, LRP6
positive regulation of cell cycle (GO:0045787)	3.94	2	LRP6, MSX1
cellular macromolecule localization (GO:0070727)	3.1	2	LRP6, MSX1
response to growth factor (GO:0070848)	4.14	2	WNT10A, PAX9
positive regulation of molecular function (GO:0044093)	2.23	2	EDA, LRP6
negative regulation of molecular function (GO:0044092)	2.74	2	LRP6, MSX1
macromolecule localization (GO:0033036)	2.34	2	LRP6, MSX1
mesenchymal cell differentiation (GO:0048762)	6.51	2	WNT10A, LRP6
negative regulation of cell death (GO:0060548)	2.95	2	LRP6, MSX1
heterocycle metabolic process (GO:0046483)	1.31	2	PAX9, MSX1
Wnt signaling pathway (GO:0016055)	3.88	2	WNT10A, LRP6
aromatic compound biosynthetic process (GO:0019438)	1.7	2	PAX9, MSX1
regulation of canonical Wnt signaling pathway (GO:0060828)	4.26	2	EDA, LRP6
negative regulation of biosynthetic process (GO:0009890)	2.47	2	PAX9, MSX1
positive regulation of canonical Wnt signaling pathway (GO:0090263)	4.95	2	EDA, LRP6
positive regulation of Wnt signaling pathway (GO:0030177)	4.7	2	EDA, LRP6
nitrogen compound metabolic process (GO:0006807)	1.13	2	PAX9, MSX1
regulation of apoptotic process (GO:0042981)	2.5	2	LRP6, MSX1
nucleic acid-templated transcription (GO:0097659)	1.91	2	PAX9, MSX1
organic substance biosynthetic process (GO:1901576)	1.34	2	PAX9, MSX1
cell morphogenesis involved in differentiation (GO:0000904)	4.67	2	LRP6, MSX1
cell morphogenesis (GO:0000902)	4.35	2	LRP6, MSX1
cellular macromolecule metabolic process (GO:0044260)	0.93	2	PAX9, MSX1
cellular component organization (GO:0016043)	1.24	2	LRP6, MSX1
cellular component organization or biogenesis (GO:0071840)	1.22	2	LRP6, MSX1
transcription from RNA polymerase II promoter (GO:0006366)	3.38	2	PAX9, MSX1
regulation of biological quality (GO:0065008)	1.68	2	LRP6, MSX1
anatomical structure formation involved in morphogenesis (GO:0048646)	3.01	2	EDA, LRP6
heterocycle biosynthetic process (GO:0018130)	1.7	2	PAX9, MSX1
nucleobase-containing compound biosynthetic process (GO:0034654)	1.72	2	PAX9, MSX1
positive regulation of intracellular signal transduction (GO:1902533)	2.95	2	EDA, MSX1
regulation of intracellular signal transduction (GO:1902531)	2.31	2	EDA, MSX1
RNA metabolic process (GO:0016070)	1.59	2	PAX9, MSX1
cellular nitrogen compound biosynthetic process (GO:0044271)	1.59	2	PAX9, MSX1
transcription, DNA-templated (GO:0006351)	1.91	2	PAX9, MSX1
negative regulation of macromolecule biosynthetic process (GO:0010558)	2.53	2	PAX9, MSX1
RNA biosynthetic process (GO:0032774)	1.84	2	PAX9, MSX1
tube formation (GO:0035148)	4.98	2	EDA, LRP6
cellular biosynthetic process (GO:0044249)	1.37	2	PAX9, MSX1
cellular nitrogen compound metabolic process (GO:0034641)	1.22	2	PAX9, MSX1
cellular macromolecule biosynthetic process (GO:0034645)	1.66	2	PAX9, MSX1
response to endogenous stimulus (GO:0009719)	2.79	2	WNT10A, LRP6
nucleobase-containing compound metabolic process (GO:0006139)	1.35	2	PAX9, MSX1
hair follicle development (GO:0001942)	6.02	2	EDA, WNT10A
biological adhesion (GO:0022610)	2.81	2	EDA, LRP6
cellular aromatic compound metabolic process (GO:0006725)	1.3	2	PAX9, MSX1
negative regulation of nucleic acid-templated transcription (GO:1903507)	2.71	2	PAX9, MSX1
negative regulation of transcription, DNA-templated (GO:0045892)	2.75	2	PAX9, MSX1
positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	4.29	2	EDA, LRP6
regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	3.83	2	EDA, LRP6
cellular response to growth factor stimulus (GO:0071363)	4.27	2	WNT10A, PAX9
negative regulation of RNA metabolic process (GO:0051253)	2.66	2	PAX9, MSX1
negative regulation of gene expression (GO:0010629)	2.48	2	PAX9, MSX1
gland development (GO:0048732)	4.15	2	EDA, WNT10A
negative regulation of cellular biosynthetic process (GO:0031327)	2.49	2	PAX9, MSX1
palate development (GO:0060021)	5.38	2	LRP6, MSX1
nucleic acid metabolic process (GO:0090304)	1.46	2	PAX9, MSX1
molting cycle process (GO:0022404)	5.54	2	EDA, WNT10A
hair cycle process (GO:0022405)	5.54	2	EDA, WNT10A
regulation of cell death (GO:0010941)	2.43	2	LRP6, MSX1
pattern specification process (GO:0007389)	3.79	2	LRP6, MSX1
negative regulation of cellular macromolecule biosynthetic process (GO:2000113)	2.6	2	PAX9, MSX1
cellular component morphogenesis (GO:0032989)	3.5	2	LRP6, MSX1
regulation of programmed cell death (GO:0043067)	2.49	2	LRP6, MSX1
negative regulation of apoptotic process (GO:0043066)	3.04	2	LRP6, MSX1
negative regulation of programmed cell death (GO:0043069)	3.02	2	LRP6, MSX1
skin development (GO:0043588)	5.84	2	EDA, WNT10A
embryonic morphogenesis (GO:0048598)	3.72	2	LRP6, MSX1
negative regulation of nucleobase-containing compound metabolic process (GO:0045934)	2.55	2	PAX9, MSX1
neuron differentiation (GO:0030182)	4.17	2	WNT10A, LRP6
morphogenesis of an epithelium (GO:0002009)	4.08	2	WNT10A, LRP6
cellular protein localization (GO:0034613)	3.11	2	LRP6, MSX1
negative regulation of RNA biosynthetic process (GO:1902679)	2.7	2	PAX9, MSX1
biosynthetic process (GO:0009058)	1.32	2	PAX9, MSX1
macromolecule biosynthetic process (GO:0009059)	1.61	2	PAX9, MSX1
negative regulation of nitrogen compound metabolic process (GO:0051172)	2.47	2	PAX9, MSX1
cell adhesion (GO:0007155)	2.82	2	EDA, LRP6
localization (GO:0051179)	1.4	2	LRP6, MSX1
cellular localization (GO:0051641)	2.32	2	LRP6, MSX1
primary metabolic process (GO:0044238)	0.69	2	PAX9, MSX1
regulation of cell cycle (GO:0051726)	2.93	2	LRP6, MSX1
cellular metabolic process (GO:0044237)	0.69	2	PAX9, MSX1
epithelial to mesenchymal transition (GO:0001837)	5.76	2	LRP6, MSX1
cartilage morphogenesis (GO:0060536)	7.33	2	LRP6, MSX1

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
regulation of anatomical structure morphogenesis (GO:0022603)	-	2.79	0.006	EDA, MSX1, WNT10A, LRP6, PAX9
bone morphogenesis (GO:0060349)	NEW	6.2	0.011	LRP6, MSX1
tube formation (GO:0035148)	-	4.98	0.05	EDA, LRP6, MSX1
face morphogenesis (GO:0060325)	-	6.29	0.001	MSX1, PAX9, LRP6
anatomical structure morphogenesis (GO:0009653)	-	2.53	0.001	EDA, MSX1, WNT10A, LRP6, PAX9
neural crest cell differentiation (GO:0014033)	-	7.94	0.008	WNT10A, LRP6
regulation of odontogenesis (GO:0042481)	-	6.55	0.0	EDA, WNT10A, MSX1, PAX9
midbrain development (GO:0030901)	NEW	6.17	0.015	LRP6, MSX1
tissue morphogenesis (GO:0048729)	-	3.87	0.038	WNT10A, MSX1, LRP6
cell surface receptor signaling pathway involved in heart development (GO:0061311)	NEW	6.96	0.047	LRP6, MSX1
ectodermal placode formation (GO:0060788)	NEW	7.02	0.004	EDA, LRP6
mesenchymal cell differentiation (GO:0048762)	-	6.51	0.009	WNT10A, LRP6
organ morphogenesis (GO:0009887)	-	3.55	0.0	EDA, MSX1, WNT10A, PAX9, LRP6
neuron differentiation (GO:0030182)	-	4.17	0.019	EDA, WNT10A, MSX1, LRP6
epithelium development (GO:0060429)	NEW	4.57	0.025	EDA, WNT10A, MSX1, LRP6
tissue development (GO:0009888)	-	3.27	0.004	EDA, MSX1, WNT10A, LRP6, PAX9
embryonic forelimb morphogenesis (GO:0035115)	NEW	6.26	0.015	LRP6, MSX1
embryonic hindlimb morphogenesis (GO:0035116)	NEW	6.36	0.013	LRP6, MSX1
forelimb morphogenesis (GO:0035136)	NEW	6.04	0.022	LRP6, MSX1
hindlimb morphogenesis (GO:0035137)	NEW	6.12	0.022	LRP6, MSX1
regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	-	3.83	0.041	EDA, WNT10A, LRP6, MSX1
odontogenesis of dentin-containing tooth (GO:0042475)	-	5.52	0.013	EDA, LRP6, MSX1
odontogenesis (GO:0042476)	-	5.19	0.0	EDA, WNT10A, PAX9, LRP6, MSX1
anatomical structure development (GO:0048856)	-	1.58	0.033	EDA, MSX1, WNT10A, PAX9, LRP6
epithelial to mesenchymal transition (GO:0001837)	-	5.76	0.036	LRP6, MSX1
cellular response to retinoic acid (GO:0071300)	NEW	5.52	0.009	EDA, LRP6, MSX1
regulation of organ morphogenesis (GO:2000027)	-	4.22	0.0	EDA, WNT10A, LRP6, PAX9, MSX1
cartilage morphogenesis (GO:0060536)	-	7.33	0.016	LRP6, MSX1
gland development (GO:0048732)	-	4.15	0.02	EDA, WNT10A, LRP6, MSX1

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

Shared terms

GO	IC	Number of genes with the same GO	Genes
intracellular membrane-bounded organelle (GO:0043231)	0.6	4	EDA, MSX1, LRP6, PAX9
cell part (GO:0044464)	0.11	4	EDA, MSX1, LRP6, PAX9
intracellular organelle (GO:0043229)	0.51	4	EDA, LRP6, PAX9, MSX1
intracellular part (GO:0044424)	0.28	4	EDA, MSX1, PAX9, LRP6
membrane-bounded organelle (GO:0043227)	0.47	4	EDA, MSX1, LRP6, PAX9
organelle (GO:0043226)	0.4	4	EDA, MSX1, LRP6, PAX9
intracellular organelle part (GO:0044446)	0.81	3	EDA, LRP6, MSX1
extracellular region (GO:0005576)	2.18	3	EDA, WNT10A, LRP6
organelle part (GO:0044422)	0.79	3	EDA, LRP6, MSX1
protein complex (GO:0043234)	1.51	2	EDA, LRP6
macromolecular complex (GO:0032991)	1.35	2	EDA, LRP6
integral component of membrane (GO:0016021)	1.14	2	EDA, LRP6
membrane (GO:0016020)	0.68	2	EDA, LRP6
cytoplasmic part (GO:0044444)	0.82	2	EDA, LRP6
plasma membrane (GO:0005886)	1.39	2	EDA, LRP6
membrane part (GO:0044425)	0.95	2	EDA, LRP6
plasma membrane part (GO:0044459)	1.95	2	EDA, LRP6
nucleus (GO:0005634)	1.07	2	PAX9, MSX1
intrinsic component of membrane (GO:0031224)	1.13	2	EDA, LRP6