Disease table of SCHIZENCEPHALY OMIM ID: 269160

Gene-disease associations table

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Gene	Associated with SCHIZENCEPHALY in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
COL4A1	HUMSAVAR	HGNC link	13q34	6	611773, 269160, PS175780, 607595, 614519, 180000
EMX2	OMIM	HGNC link	10q26.11	1	269160
SHH	OMIM	HGNC link	7q36.3	4	PS300345, 269160, PS236100, 147250
SIX3	OMIM, HUMSAVAR	HGNC link	2p21	3	269160, PS236100, 147250

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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
SHH	YES	3	STAT3, PAX3, SOX9
EMX2	YES	2	HOXA10, PBX2
COL4A1	YES	1	LMX1B
SIX3	YES	2	PAX6, PROX1

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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
SHH	SIX3	Yes	activation, binding	7	SALL1, PITX2, PLP1, POU3F4, BMP4, WNT1, PAX6
SHH	EMX2	No	-	3	WNT1, FGF8, EGFR
SHH	COL4A1	No	-	2	BMP2, BMP4
EMX2	SIX3	No	-	1	WNT1
COL4A1	SIX3	No	-	1	BMP4

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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

KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Pathways in cancer	hsa05200	3.98	2	SHH, COL4A1

REACTOME pathways annotation: shared terms / 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	2	SHH, COL4A1

NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Anchoring fibril formation (R-HSA-2214320)	NEW	9.08	0.002	SHH, COL4A1
Regulation of beta-cell development (R-HSA-186712)	NEW	7.98	0.04	SHH, EMX2

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GO - molecular function annotation: shared terms (no NET-GE enrichment)

Shared terms

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GO	IC	Number of genes with the same GO	Genes
sequence-specific DNA binding (GO:0043565)	2.79	2	SIX3, EMX2
DNA binding (GO:0003677)	1.92	2	SIX3, EMX2
nucleic acid binding (GO:0003676)	1.44	2	SIX3, EMX2
heterocyclic compound binding (GO:1901363)	1.06	2	SIX3, EMX2
organic cyclic compound binding (GO:0097159)	1.05	2	SIX3, EMX2
protein binding (GO:0005515)	0.46	4	SHH, COL4A1, EMX2, SIX3
binding (GO:0005488)	0.18	4	SHH, COL4A1, EMX2, 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
telencephalon regionalization (GO:0021978)	7.78	2	SHH, SIX3
cell proliferation in forebrain (GO:0021846)	6.96	2	SIX3, EMX2
renal system development (GO:0072001)	6.73	2	SHH, EMX2
patterning of blood vessels (GO:0001569)	6.4	2	SHH, COL4A1
regulation of neuroblast proliferation (GO:1902692)	6.36	2	SHH, SIX3
neural precursor cell proliferation (GO:0061351)	5.7	3	SHH, SIX3, EMX2
dorsal/ventral pattern formation (GO:0009953)	5.6	2	SHH, SIX3
regulation of stem cell proliferation (GO:0072091)	5.6	2	SHH, SIX3
forebrain development (GO:0030900)	5.48	2	SHH, EMX2
regulation of neural precursor cell proliferation (GO:2000177)	5.45	2	SHH, SIX3

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
cerebral cortex regionalization (GO:0021796)	NEW	7.94	0.014	SHH, EMX2
forebrain dorsal/ventral pattern formation (GO:0021798)	NEW	7.78	0.004	SHH, SIX3
positive regulation of oligodendrocyte differentiation (GO:0048714)	NEW	7.16	0.019	SHH, EMX2
cardiac muscle cell proliferation (GO:0060038)	NEW	7.16	0.038	SHH, EMX2
striated muscle cell proliferation (GO:0014855)	NEW	7.02	0.047	SHH, EMX2
cell proliferation in forebrain (GO:0021846)	-	6.96	0.029	SHH, EMX2
renal system development (GO:0072001)	-	6.73	0.002	SHH, EMX2
patterning of blood vessels (GO:0001569)	-	6.4	0.013	SHH, COL4A1
embryonic skeletal system development (GO:0048706)	NEW	5.97	0.002	SHH, SIX3, EMX2
neural precursor cell proliferation (GO:0061351)	-	5.7	0.021	SHH, EMX2

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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 lumen (GO:0005788)	4.5	2	SHH, COL4A1
proteinaceous extracellular matrix (GO:0005578)	4.01	2	SHH, COL4A1
extracellular matrix (GO:0031012)	3.81	2	SHH, COL4A1
organelle lumen (GO:0043233)	3.05	2	SHH, COL4A1
intracellular organelle lumen (GO:0070013)	3.05	2	SHH, COL4A1
membrane-enclosed lumen (GO:0031974)	3.05	2	SHH, COL4A1
endoplasmic reticulum part (GO:0044432)	2.73	2	SHH, COL4A1
extracellular region (GO:0005576)	2.18	2	SHH, COL4A1
extracellular region part (GO:0044421)	1.57	2	SHH, COL4A1
nucleus (GO:0005634)	1.07	2	SIX3, EMX2

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
endoplasmic reticulum lumen (GO:0005788)	-	4.5	0.008	SHH, COL4A1, EMX2
extracellular matrix (GO:0031012)	-	3.81	0.038	SHH, COL4A1, EMX2

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