Disease table of MICROPHTHALMIA, SYNDROMIC OMIM ID: PS309800

Gene-disease associations table

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Gene	Associated with MICROPHTHALMIA, SYNDROMIC in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
BCOR	ClinVar, OMIM, HUMSAVAR	HGNC link	Xp11.4	1	PS309800
BMP4	ClinVar, OMIM, HUMSAVAR	HGNC link	14q22.2	2	PS309800, PS119530
HCCS	ClinVar, OMIM, HUMSAVAR	HGNC link	Xp22.2	2	PS309800, PS309801
HMGB3	ClinVar, OMIM	HGNC link	Xq28	1	PS309800
MAB21L2	ClinVar, OMIM, HUMSAVAR	HGNC link	4q31.3	1	PS309800
NAA10	ClinVar, OMIM	HGNC link	Xq28	2	300855, PS309800
OTX2	ClinVar, OMIM, HUMSAVAR	HGNC link	14q22.3	2	PS309800, PS613038
RARB	ClinVar, OMIM, HUMSAVAR	HGNC link	3p24.2	1	PS309800
SOX2	ClinVar, OMIM	HGNC link	3q26.33	1	PS309800
STRA6	ClinVar, OMIM, HUMSAVAR	HGNC link	15q24.1	2	PS309800, PS300345

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Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By sub-band

Shared sub_band	Number of genes associated with the disease	Genes associated with the disease
Xq28	2	HMGB3, NAA10

By band

Shared band	Number of genes associated with the disease	Genes associated with the disease
14q22	2	BMP4, OTX2
Xq28	2	HMGB3, NAA10

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
14q2	2	BMP4, OTX2
Xq2	2	HMGB3, NAA10

By arm

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Shared arm	Number of genes associated with the disease	Genes associated with the disease
14q	2	BMP4, OTX2
Xp	2	BCOR, HCCS
Xq	2	HMGB3, NAA10

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By chromosome

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Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
14	2	BMP4, OTX2
3	2	SOX2, RARB
X	4	HMGB3, NAA10, HCCS, BCOR

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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
OTX2	YES	12	TYR, POU1F1, HESX1, DCT, BEST1, AURKA, RBP3, IL6, CCNG2, IGF1, PAX6, CDC25C	0
RARB	YES	3	RARB, ADH5, THBD	1	RARB
SOX2	YES	24	POU4F2, ISL1, NTRK3, FGF4, VIM, TUBB3, LHX3, ITGA6, CCND1, L1TD1, PGA5, DKK1, PAX6, MKI67, RHO, ABCC6, PLAC1, UTF1, ABCC3, POU1F1, LXN, MMP3, SEMA6A, ASXL1	0
POU5F1	NO	26	TBX18, BMP4, FGF4, TDGF1, NR0B1, GATA6, ITGA6, DDC, L1TD1, DKK1, CDKN1A, CDX2, LEFTY1, SOX2, ID2, SPP1, UTF1, NANOG, T, HLX, DLX5, EOMES, THY1, GADD45A, ZFP42, SEMA6A	2	BMP4, SOX2

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regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
BMP4	YES	4	POU5F1, FOXL1, ETS1, GATA4	0
RARB	YES	7	RARB, HDAC1, RARA, FOXD3, JUN, PPARG, RARG	1	RARB
SOX2	YES	1	POU5F1	0
POU1F1	NO	7	OTX2, SOX2, HMGA1, LHX4, POU1F1, HMGA2, LHX2	2	OTX2, SOX2
PAX6	NO	7	SP1, CTCF, OTX2, SOX2, TFCP2, FOXA2, SIRT1	2	OTX2, SOX2

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
NAA10	BCOR	Yes	1	BCOR
HCCS	SOX2	No	1	FZR1
NAA10	STRA6	No	1	NTRK1
NAA10	RARB	No	1	MEOX2
NAA10	SOX2	No	2	MTA1, EHMT2
HMGB3	SOX2	No	1	SUPT16H
MAB21L2	OTX2	No	1	APP
MAB21L2	SOX2	No	2	MEIS2, PBX2
RARB	BCOR	No	1	NCOR2
RARB	SOX2	No	2	NCOR2, ARID1A

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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
BMP4	OTX2	No	-	5	WNT5A, WNT1, FGF8, MYC, MITF
BMP4	RARB	No	-	1	FGF10
BMP4	SOX2	No	-	18	STAT3, DKK1, EOMES, FGFR1, KLF4, NKX2-1, FGF8, CDX1, FGF4, PROM1, SMAD4, CDX2, YBX1, PAX6, CCND1, NOG, HMGA2, TBX2
STRA6	RARB	No	-	1	PGR
OTX2	SOX2	No	-	3	FGF2, FGF8, FOXM1
RARB	SOX2	No	-	1	NR5A1

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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 (no NET-GE enrichment)

Shared terms

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KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Signaling pathways regulating pluripotency of stem cells	hsa04550	5.6	2	BMP4, SOX2
Hippo signaling pathway	hsa04390	5.37	2	BMP4, SOX2
Pathways in cancer	hsa05200	3.98	2	RARB, BMP4

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REACTOME pathways annotation: shared terms (no NET-GE enrichment)

Shared terms

REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Signal Transduction	R-HSA-162582	1.78	3	STRA6, RARB, SOX2

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
structure-specific DNA binding (GO:0043566)	4.98	2	HMGB3, VAX1
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0001077)	4.31	2	OTX2, SOX2
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding (GO:0001228)	3.98	2	OTX2, SOX2
transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding (GO:0000982)	3.94	2	OTX2, SOX2
transcription factor binding (GO:0008134)	3.46	2	RARB, BCOR
RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	3.37	3	RARB, OTX2, VAX1
RNA polymerase II regulatory region DNA binding (GO:0001012)	3.36	3	RARB, OTX2, VAX1
RNA polymerase II transcription factor activity, sequence-specific DNA binding (GO:0000981)	3.29	4	RARB, OTX2, VAX1, SOX2
transcription regulatory region sequence-specific DNA binding (GO:0000976)	3.24	4	RARB, OTX2, VAX1, SOX2
sequence-specific double-stranded DNA binding (GO:1990837)	3.2	4	RARB, OTX2, VAX1, SOX2

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
receptor agonist activity (GO:0048018)	NEW	6.97	0.028	OTX2, BMP4
transcription regulatory region DNA binding (GO:0044212)	-	3.03	0.008	RARB, OTX2, BCOR, SOX2
regulatory region nucleic acid binding (GO:0001067)	-	3.03	0.009	RARB, OTX2, BCOR, SOX2
regulatory region DNA binding (GO:0000975)	-	3.03	0.009	RARB, OTX2, BCOR, SOX2

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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
smooth muscle tissue development (GO:0048745)	7.02	2	STRA6, BMP4
glandular epithelial cell development (GO:0002068)	6.96	2	RARB, BMP4
negative regulation of chondrocyte differentiation (GO:0032331)	6.78	2	RARB, BMP4
embryonic digestive tract development (GO:0048566)	6.78	2	STRA6, RARB
regulation of odontogenesis (GO:0042481)	6.55	2	BCOR, BMP4
negative regulation of cartilage development (GO:0061037)	6.51	2	RARB, BMP4
embryonic hindlimb morphogenesis (GO:0035116)	6.36	2	RARB, BMP4
pituitary gland development (GO:0021983)	6.33	2	BMP4, SOX2
columnar/cuboidal epithelial cell development (GO:0002066)	6.29	2	RARB, BMP4
lung alveolus development (GO:0048286)	6.15	2	STRA6, BMP4

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
diencephalon morphogenesis (GO:0048852)	NEW	9.73	0.001	OTX2, SOX2
paramesonephric duct development (GO:0061205)	NEW	8.63	0.028	STRA6, BMP4
lens induction in camera-type eye (GO:0060235)	NEW	8.34	0.023	BMP4, SOX2
specification of axis polarity (GO:0065001)	NEW	8.12	0.028	BCOR, BMP4
mesenchymal cell differentiation involved in renal system development (GO:2001012)	NEW	7.65	0.049	BMP4, SOX2
mesenchymal cell differentiation involved in kidney development (GO:0072161)	NEW	7.65	0.049	BMP4, SOX2
negative regulation of stem cell proliferation (GO:2000647)	NEW	7.33	0.029	VAX1, BMP4
smooth muscle tissue development (GO:0048745)	-	7.02	0.029	STRA6, BMP4
glandular epithelial cell development (GO:0002068)	-	6.96	0.029	RARB, OTX2, BMP4
embryonic digestive tract development (GO:0048566)	-	6.78	0.037	STRA6, RARB

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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
mitochondrion (GO:0005739)	2.42	2	HCCS, BCOR
nucleoplasm (GO:0005654)	1.89	2	RARB, SOX2
non-membrane-bounded organelle (GO:0043228)	1.76	2	HMGB3, NAA10
intracellular non-membrane-bounded organelle (GO:0043232)	1.76	2	HMGB3, NAA10
nuclear part (GO:0044428)	1.55	4	RARB, NAA10, SOX2, BCOR
protein complex (GO:0043234)	1.51	5	STRA6, BCOR, OTX2, NAA10, SOX2
macromolecular complex (GO:0032991)	1.35	5	STRA6, BCOR, OTX2, NAA10, SOX2
nucleus (GO:0005634)	1.07	8	RARB, OTX2, VAX1, NAA10, HMGB3, SOX2, BCOR, MAB21L2
cytoplasm (GO:0005737)	1.01	5	NAA10, HMGB3, BMP4, SOX2, RARB
cytoplasmic part (GO:0044444)	0.82	4	NAA10, HCCS, BCOR, SOX2

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