Disease table of HOLOPROSENCEPHALY OMIM ID: PS236100

Gene-disease associations table

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Gene	Associated with HOLOPROSENCEPHALY in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
CDON	ClinVar, OMIM, HUMSAVAR	HGNC link	11q24.2	1	PS236100
GAS1	ClinVar	HGNC link	9q21.33	1	PS236100
GLI2	ClinVar, OMIM, HUMSAVAR	HGNC link	2q14.2	2	PS236100, 615849
PTCH1	ClinVar, OMIM, HUMSAVAR	HGNC link	9q22.32	4	605462, 109400, PS142623, PS236100
SHH	ClinVar, OMIM, HUMSAVAR	HGNC link	7q36.3	4	PS300345, 269160, PS236100, 147250
SIX3	ClinVar, OMIM, HUMSAVAR	HGNC link	2p21	3	269160, PS236100, 147250
TGIF1	ClinVar, OMIM, HUMSAVAR	HGNC link	18p11.31	1	PS236100
ZIC2	ClinVar, OMIM, HUMSAVAR	HGNC link	13q32.3	1	PS236100

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Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
9q2	2	GAS1, PTCH1

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
9q	2	GAS1, PTCH1

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
2	2	SIX3, GLI2
9	2	GAS1, PTCH1

Transcription Factors (TF) annotation from TRRUST

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TF	associated to this disease	# regulated genes	Regulated genes
GLI2	YES	14	WNT2B, FOXC2, MUC5AC, BCL2, FAS, FOXL1, TNFRSF10B, FST, FOXF1, JUN, FOXA2, FOXE1, PDGFRA, H2AFX
ZIC2	YES	1	SLC13A4
TGIF1	YES	2	SOX3, SERPINE1

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regulated gene	associated to this disease	# TFs	TFs
SIX3	YES	2	PAX6, PROX1
GLI2	YES	3	SMAD3, TP53, CTNNB1
SHH	YES	3	STAT3, PAX3, SOX9
TGIF1	YES	2	HDAC4, SOX3

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
GLI2	ZIC2	Yes	0
GLI2	TGIF1	No	1	HDAC1
ZIC2	GAS1	No	1	ELAVL1
ZIC2	TGIF1	No	1	ELAVL1
GAS1	TGIF1	No	1	ELAVL1

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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
SIX3	SHH	Yes	activation, binding	7	SALL1, PITX2, PLP1, POU3F4, BMP4, WNT1, PAX6
GLI2	SHH	Yes	activation, binding	29	WNT2B, RUNX2, WNT5A, PTCH1, MYF5, FOXA2, GAST, WNT3A, WNT5B, JAG1, CDON, PRKCD, SMO, WNT1, GLI1, WNT16, GLI3, PTCH2, WNT7A, AKT1, MYOD1, WNT3, WNT2, ZIC2, BMP2, WNT7B, ASCL1, MAP2K1, WNT4
GLI2	CDON	Yes	activation, binding	3	DHH, SHH, IHH
GLI2	ZIC2	Yes	binding	3	SHH, GLI1, GLI3
GLI2	PTCH1	Yes	activation, binding	7	DHH, BMP2, SMO, IHH, GLI1, GLI3, SHH
SHH	CDON	Yes	activation, binding	1	GLI2
SHH	ZIC2	Yes	expression, activation, binding	3	GLI3, GLI2, GLI1
SHH	GAS1	Yes	activation, binding	1	FOXM1
SHH	PTCH1	Yes	activation	14	CDK1, STIL, BMP4, FGF10, SMO, TGFB2, GLI3, GLI2, GLI1, CCNB1, BMP2, UBC, GPC3, GPC5
SIX3	GLI2	No	-	2	SHH, WNT1

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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
Hedgehog signaling pathway	hsa04340	7.01	5	SHH, ZIC2, PTCH1, GLI2, GAS1
Basal cell carcinoma	hsa05217	6.79	3	SHH, PTCH1, GLI2
Pathways in cancer	hsa05200	3.98	3	SHH, PTCH1, GLI2

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Hedgehog signaling pathway (hsa04340)	-	7.01	0.0	CDON, PTCH1, GAS1, ZIC2, GLI2, SHH
Basal cell carcinoma (hsa05217)	-	6.79	0.003	SHH, PTCH1, GLI2
Cancers: Specific types	NEW	4.1	0.022	SHH, PTCH1, GLI2
Pathways in cancer (hsa05200)	-	3.98	0.027	SHH, PTCH1, GLI2
Signal transduction	NEW	2.06	0.009	SHH, ZIC2, PTCH1, GLI2, GAS1
Environmental Information Processing	NEW	1.71	0.032	SHH, ZIC2, PTCH1, GLI2, GAS1

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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
Ligand-receptor interactions	R-HSA-5632681	9.98	4	SHH, PTCH1, CDON, GAS1
Hedgehog 'on' state	R-HSA-5632684	6.62	5	GAS1, SHH, PTCH1, CDON, GLI2
Class B/2 (Secretin family receptors)	R-HSA-373080	6.52	2	SHH, PTCH1
Hedgehog 'off' state	R-HSA-5610787	6.19	2	PTCH1, GLI2
Signaling by Hedgehog	R-HSA-5358351	5.79	5	GAS1, SHH, PTCH1, CDON, GLI2
GPCR ligand binding	R-HSA-500792	4.19	2	SHH, PTCH1
Signaling by GPCR	R-HSA-372790	2.68	2	SHH, PTCH1
Signal Transduction	R-HSA-162582	1.78	6	CDON, PTCH1, GAS1, GLI2, SHH, TGIF1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Ligand-receptor interactions (R-HSA-5632681)	-	9.98	0.0	SHH, PTCH1, CDON, GAS1
CDO in myogenesis (R-HSA-375170)	NEW	8.12	0.038	SHH, CDON
Myogenesis (R-HSA-525793)	NEW	8.12	0.038	SHH, CDON
Hedgehog 'on' state (R-HSA-5632684)	-	6.62	0.0	SHH, PTCH1, GLI2, GAS1, CDON
Class B/2 (Secretin family receptors) (R-HSA-373080)	-	6.52	0.028	SHH, PTCH1, GLI2
Signaling by Hedgehog (R-HSA-5358351)	-	5.79	0.0	SHH, PTCH1, GLI2, GAS1, CDON
Signal Transduction (R-HSA-162582)	-	1.78	0.015	CDON, PTCH1, GAS1, GLI2, SHH, TGIF1

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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
patched binding (GO:0005113)	7.66	2	SHH, PTCH1
glycosaminoglycan binding (GO:0005539)	4.42	2	SHH, PTCH1
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228)	3.98	2	SIX3, GLI2
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0000982)	3.94	2	TGIF1, GLI2
RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	3.88	2	TGIF1, GLI2
core promoter proximal region sequence-specific DNA binding (GO:0000987)	3.83	2	TGIF1, GLI2
core promoter proximal region DNA binding (GO:0001159)	3.82	2	TGIF1, GLI2
chromatin binding (GO:0003682)	3.64	2	ZIC2, GLI2
transcription cofactor activity (GO:0003712)	3.44	2	SIX3, TGIF1
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	3.37	3	TGIF1, GLI2, SIX3

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
hedgehog family protein binding (GO:0097108)	NEW	8.64	0.0	SHH, PTCH1
patched binding (GO:0005113)	-	7.66	0.001	SHH, PTCH1
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	NEW	5.23	0.018	SHH, SIX3, ZIC2
structure-specific DNA binding (GO:0043566)	NEW	4.98	0.012	SHH, ZIC2, GLI2, SIX3
RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)	NEW	4.84	0.027	SHH, SIX3, TGIF1
chromatin binding (GO:0003682)	-	3.64	0.0	SIX3, PTCH1, ZIC2, GLI2, SHH, TGIF1
transcription factor binding (GO:0008134)	NEW	3.46	0.006	SHH, TGIF1, ZIC2, GLI2, SIX3
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	-	3.37	0.001	SHH, TGIF1, ZIC2, GLI2, SIX3
RNA polymerase II regulatory region DNA binding (GO:0001012)	-	3.36	0.001	SHH, TGIF1, ZIC2, GLI2, SIX3
sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	-	3.29	0.004	SHH, TGIF1, ZIC2, GLI2, SIX3

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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
ventral midline development (GO:0007418)	8.63	2	SHH, GLI2
hindgut morphogenesis (GO:0007442)	8.34	2	SHH, GLI2
smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)	8.34	2	SHH, GLI2
spinal cord dorsal/ventral patterning (GO:0021513)	8.12	2	SHH, GLI2
mammary gland duct morphogenesis (GO:0060603)	7.94	2	PTCH1, GLI2
smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	7.78	2	PTCH1, GLI2
cell proliferation involved in metanephros development (GO:0072203)	7.78	2	SHH, PTCH1
telencephalon regionalization (GO:0021978)	7.78	2	SHH, SIX3
cell proliferation involved in kidney development (GO:0072111)	7.43	2	SHH, PTCH1
positive regulation of T cell differentiation in thymus (GO:0033089)	7.24	2	SHH, GLI2

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
cell-cell signaling involved in cell fate commitment (GO:0045168)	NEW	9.04	0.003	SHH, SIX3, GLI2
response to chlorate (GO:0010157)	NEW	9.04	0.002	SHH, PTCH1
spinal cord ventral commissure morphogenesis (GO:0021965)	NEW	9.04	0.001	PTCH1, GLI2
ventral midline development (GO:0007418)	-	8.63	0.0	SHH, GLI2
hindgut morphogenesis (GO:0007442)	-	8.34	0.002	SHH, GLI2
smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)	-	8.34	0.002	SHH, GLI2
prostatic bud formation (GO:0060513)	NEW	8.34	0.006	SHH, GLI2
spinal cord dorsal/ventral patterning (GO:0021513)	-	8.12	0.003	SHH, GLI2
mammary gland duct morphogenesis (GO:0060603)	-	7.94	0.002	PTCH1, GLI2
forebrain dorsal/ventral pattern formation (GO:0021798)	NEW	7.78	0.021	SHH, SIX3

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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
primary cilium (GO:0072372)	4.64	2	PTCH1, GLI2
membrane raft (GO:0045121)	4.18	2	SHH, PTCH1
membrane microdomain (GO:0098857)	4.17	2	SHH, PTCH1
ciliary part (GO:0044441)	4.05	2	PTCH1, GLI2
membrane region (GO:0098589)	3.95	2	SHH, PTCH1
cilium (GO:0005929)	3.89	2	PTCH1, GLI2
extracellular matrix (GO:0031012)	3.81	2	SHH, CDON
cell surface (GO:0009986)	3.44	2	SHH, CDON
cell projection part (GO:0044463)	2.97	2	PTCH1, GLI2
intrinsic component of plasma membrane (GO:0031226)	2.53	2	CDON, GAS1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
primary cilium (GO:0072372)	-	4.64	0.038	PTCH1, GLI2
proteinaceous extracellular matrix (GO:0005578)	NEW	4.01	0.015	SHH, PTCH1, CDON, GLI2
extracellular matrix (GO:0031012)	-	3.81	0.035	SHH, PTCH1, CDON, GLI2

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