Disease table of MICROPHTHALMIA, ISOLATED, WITH COLOBOMA OMIM ID: PS300345

Gene-disease associations table

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Gene	Associated with MICROPHTHALMIA, ISOLATED, WITH COLOBOMA in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
ABCB6	ClinVar, OMIM, HUMSAVAR	HGNC link	2q35	4	PS127500, 609153, 111600, PS300345
GDF3	ClinVar, OMIM, HUMSAVAR	HGNC link	12p13.31	4	PS300345, PS118100, 120200, PS251600
GDF6	ClinVar, OMIM	HGNC link	8q22.1	4	PS300345, PS118100, PS204000, PS251600
RBP4	ClinVar, OMIM, HUMSAVAR	HGNC link	10q23.33	2	PS300345, 615147
SHH	OMIM	HGNC link	7q36.3	4	PS300345, 269160, PS236100, 147250
STRA6	ClinVar, OMIM, HUMSAVAR	HGNC link	15q24.1	2	PS309800, PS300345
TENM3	ClinVar, OMIM	HGNC link	4q34.3	1	PS300345
VSX2	ClinVar, OMIM, HUMSAVAR	HGNC link	14q24.3	2	PS251600, PS300345

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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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regulated gene	associated to this disease	# TFs	TFs
GDF3	YES	1	NANOG
VSX2	YES	1	NEUROG3
SHH	YES	3	STAT3, PAX3, SOX9

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Interactions from BIOGRID - physical

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
STRA6	RBP4	Yes	binding	1	TTR
GDF6	SHH	No	-	1	NOG
ABCB6	SHH	No	-	1	UBC
VSX2	SHH	No	-	1	ASCL1

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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 (no shared terms)

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
Retinoid cycle disease events	R-HSA-2453864	9.28	2	STRA6, RBP4
Diseases associated with visual transduction	R-HSA-2474795	9.28	2	STRA6, RBP4
The canonical retinoid cycle in rods (twilight vision)	R-HSA-2453902	8.52	2	STRA6, RBP4
Visual phototransduction	R-HSA-2187338	6.44	2	STRA6, RBP4
Diseases of signal transduction	R-HSA-5663202	4.89	3	STRA6, SHH, RBP4
Disease	R-HSA-1643685	3.33	4	STRA6, SHH, ABCB6, RBP4
Signal Transduction	R-HSA-162582	1.78	3	STRA6, SHH, RBP4

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Diseases associated with visual transduction (R-HSA-2474795)	-	9.28	0.0	STRA6, RBP4
Retinoid cycle disease events (R-HSA-2453864)	-	9.28	0.0	STRA6, RBP4
The canonical retinoid cycle in rods (twilight vision) (R-HSA-2453902)	-	8.52	0.018	STRA6, RBP4
Visual phototransduction (R-HSA-2187338)	-	6.44	0.019	STRA6, RBP4
Diseases of signal transduction (R-HSA-5663202)	-	4.89	0.004	STRA6, SHH, RBP4
Disease (R-HSA-1643685)	-	3.33	0.002	STRA6, SHH, ABCB6, RBP4

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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
vitamin transporter activity (GO:0051183)	6.56	2	STRA6, RBP4
transforming growth factor beta receptor binding (GO:0005160)	5.81	2	GDF6, GDF3
growth factor activity (GO:0008083)	4.66	2	GDF6, GDF3
cytokine activity (GO:0005125)	4.34	2	GDF6, GDF3
cytokine receptor binding (GO:0005126)	4.14	2	GDF6, GDF3
protein heterodimerization activity (GO:0046982)	3.64	2	TENM3, RBP4
protein homodimerization activity (GO:0042803)	3.16	2	TENM3, GDF6
protein dimerization activity (GO:0046983)	2.72	3	TENM3, GDF6, RBP4
identical protein binding (GO:0042802)	2.63	2	TENM3, GDF6
transporter activity (GO:0005215)	2.57	3	STRA6, ABCB6, RBP4

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
vitamin transporter activity (GO:0051183)	-	6.56	0.012	STRA6, RBP4

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
formation of anatomical boundary (GO:0048859)	8.12	2	SHH, GDF3
lung epithelium development (GO:0060428)	7.33	2	STRA6, SHH
female genitalia development (GO:0030540)	7.09	2	STRA6, RBP4
digestive tract morphogenesis (GO:0048546)	6.78	2	STRA6, SHH
genitalia development (GO:0048806)	6.2	3	STRA6, SHH, RBP4
negative regulation of muscle tissue development (GO:1901862)	6.17	2	SHH, RBP4
vasculature development (GO:0001944)	6.04	2	STRA6, SHH
embryonic skeletal system development (GO:0048706)	5.97	2	SHH, RBP4
positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)	5.86	2	GDF6, GDF3
skin development (GO:0043588)	5.84	2	SHH, ABCB6

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
retinol transport (GO:0034633)	NEW	9.73	0.0	STRA6, RBP4
isoprenoid transport (GO:0046864)	NEW	9.73	0.0	STRA6, RBP4
terpenoid transport (GO:0046865)	NEW	9.73	0.0	STRA6, RBP4
embryonic camera-type eye formation (GO:0060900)	NEW	9.04	0.003	STRA6, RBP4
nose morphogenesis (GO:0043585)	NEW	8.63	0.004	STRA6, RBP4
paramesonephric duct development (GO:0061205)	NEW	8.63	0.012	STRA6, RBP4
uterus morphogenesis (GO:0061038)	NEW	8.12	0.008	STRA6, RBP4
pulmonary artery morphogenesis (GO:0061156)	NEW	8.12	0.015	STRA6, RBP4
formation of anatomical boundary (GO:0048859)	-	8.12	0.015	SHH, GDF3
ductus arteriosus closure (GO:0097070)	NEW	7.94	0.025	STRA6, RBP4

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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
endoplasmic reticulum part (GO:0044432)	2.73	2	SHH, ABCB6
extracellular space (GO:0005615)	2.63	4	SHH, RBP4, GDF3, GDF6
extracellular region (GO:0005576)	2.18	4	SHH, RBP4, GDF3, GDF6
extracellular organelle (GO:0043230)	1.89	2	ABCB6, RBP4
extracellular vesicle (GO:1903561)	1.89	2	ABCB6, RBP4
extracellular exosome (GO:0070062)	1.89	2	ABCB6, RBP4
membrane-bounded vesicle (GO:0031988)	1.71	2	ABCB6, RBP4
cytosol (GO:0005829)	1.68	2	SHH, RBP4
vesicle (GO:0031982)	1.64	2	ABCB6, RBP4
extracellular region part (GO:0044421)	1.57	5	SHH, ABCB6, RBP4, GDF3, GDF6

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