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Cluster 109

11 diseases · 20 shared-gene connections

11 Diseases

36 Unique genes

0.176 Avg. similarity score

Congenital exomphalos Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Pinned (dragged)

Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Congenital exomphalos Sacral defect Caudal regression syndrome Congenital omphalocele Currarino syndrome Vascular brain injury

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital exomphalos	6	6	2
Sacral defect	6	6	2
Caudal regression syndrome	5	5	3
Congenital omphalocele	5	5	7
Currarino syndrome	5	5	2
Vascular brain injury	5	5	14
Neural tube defects, susceptibility to	3	3	5
15q13.3 microdeletion syndrome	2	2	2
Auditory system disease	1	1	11
Yellow nail syndrome	1	1	1
autosomal dominant cerebellar ataxia	1	1	1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵	Member diseases ⇵	Linked diseases
PCSK5	6 / 11	Caudal regression syndrome, Congenital exomphalos, Congenital omphalocele, Currarino syndrome and 2 more
CHRNA7	3 / 11	15q13.3 microdeletion syndrome, Congenital exomphalos, Congenital omphalocele
VANGL1	3 / 11	Caudal regression syndrome, Neural tube defects, susceptibility to, Sacral defect
BMAL1	2 / 11	Auditory system disease, Vascular brain injury
CELSR1	2 / 11	Neural tube defects, susceptibility to, Yellow nail syndrome
FUZ	2 / 11	Caudal regression syndrome, Neural tube defects, susceptibility to
NPTX1	2 / 11	autosomal dominant cerebellar ataxia, Vascular brain injury
RASSF10	2 / 11	Auditory system disease, Vascular brain injury

What do these columns mean?

Connections in cluster: How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners: How many of those links are statistically significant (FDR q < 0.05).
Curated genes: Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes): How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y): x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count: Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment: Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value: Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster): Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster): Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
Defective SLC2A10 causes arterial tortuosity syndrome (ATS) SLC2A10	Reactome	1 / 1	334×	3.00e-3	3.07e-2 ✓ sig.
NGF processing PCSK5	Reactome	1 / 4	83.4×	1.19e-2	7.61e-2
Activation of NIMA Kinases NEK9, NEK6, NEK7 NEK9	Reactome	1 / 7	47.7×	2.08e-2	1.05e-1
Suppression of apoptosis RNF213	Reactome	1 / 7	47.7×	2.08e-2	1.05e-1
Focal adhesion VAV3, FLNA, LAMA5	KEGG	3 / 203	4.9×	2.26e-2	1.10e-1
OAS antiviral response FLNA	Reactome	1 / 9	37.1×	2.67e-2	1.21e-1
Assembly of active LPL and LIPC lipase complexes PCSK5	Reactome	1 / 11	30.3×	3.25e-2	1.35e-1
Cell-extracellular matrix interactions FLNA	Reactome	1 / 12	27.8×	3.54e-2	1.42e-1
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors CHRNA7	Reactome	1 / 12	27.8×	3.54e-2	1.42e-1
GP1b-IX-V activation signalling FLNA	Reactome	1 / 12	27.8×	3.54e-2	1.42e-1
Glucagon signaling pathway CREB5, PGAM1	KEGG	2 / 107	6.2×	4.07e-2	1.53e-1
KSRP (KHSRP) binds and destabilizes mRNA EXOSC1	Reactome	1 / 15	22.2×	4.41e-2	1.60e-1
Cholinergic synapse CHRNA7, CREB5	KEGG	2 / 115	5.8×	4.64e-2	1.65e-1
mRNA decay by 3' to 5' exoribonuclease EXOSC1	Reactome	1 / 16	20.9×	4.69e-2	1.65e-1
Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA EXOSC1	Reactome	1 / 17	19.6×	4.98e-2	1.71e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis CELSR1, VANGL2	GO:0060488	2 / 2	519×	3.61e-6	2.31e-4 ✓ sig.
planar dichotomous subdivision of terminal units involved in lung branching morphogenesis CELSR1, VANGL2	GO:0060489	2 / 2	519×	3.61e-6	2.31e-4 ✓ sig.
lateral sprouting involved in lung morphogenesis CELSR1, VANGL2	GO:0060490	2 / 2	519×	3.61e-6	2.31e-4 ✓ sig.
establishment of planar polarity FUZ, CELSR1, VANGL2	GO:0001736	3 / 16	97.3×	3.61e-6	2.31e-4 ✓ sig.
establishment of body hair planar orientation CELSR1, VANGL2	GO:0048105	2 / 4	260×	2.16e-5	9.54e-4 ✓ sig.
Wnt signaling pathway, planar cell polarity pathway VANGL1, CELSR1, VANGL2	GO:0060071	3 / 34	45.8×	3.77e-5	1.45e-3 ✓ sig.
hair follicle development FUZ, LAMA5, VANGL2	GO:0001942	3 / 48	32.4×	1.07e-4	3.18e-3 ✓ sig.
apical protein localization CELSR1, VANGL2	GO:0045176	2 / 16	64.9×	4.26e-4	8.59e-3 ✓ sig.
neural tube closure FUZ, CELSR1, VANGL2	GO:0001843	3 / 85	18.3×	5.82e-4	1.06e-2 ✓ sig.
positive regulation of neural precursor cell proliferation RASSF10, FLNA	GO:2000179	2 / 21	49.4×	7.41e-4	1.25e-2 ✓ sig.
negative regulation of connective tissue growth factor production SLC2A10	GO:0032683	1 / 1	519×	1.93e-3	2.20e-2 ✓ sig.
negative regulation of proteoglycan biosynthetic process SLC2A10	GO:1902729	1 / 1	519×	1.93e-3	2.20e-2 ✓ sig.
regulation of membrane repolarization during atrial cardiac muscle cell action potential FLNA	GO:1905000	1 / 1	519×	1.93e-3	2.20e-2 ✓ sig.
regulation of membrane repolarization during cardiac muscle cell action potential FLNA	GO:1905031	1 / 1	519×	1.93e-3	2.20e-2 ✓ sig.
cell migration involved in kidney development VANGL2	GO:0035787	1 / 1	519×	1.93e-3	2.20e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Caudal regression syndrome	Sacral defect	0.500	2	2.53e-8	2.03e-7 ✓ sig.
Congenital exomphalos	Congenital omphalocele	0.250	2	1.77e-7	1.25e-6 ✓ sig.
Caudal regression syndrome	Neural tube defects, susceptibility to	0.286	2	2.53e-7	1.75e-6 ✓ sig.
Auditory system disease	Vascular brain injury	0.083	2	4.20e-5	2.03e-4 ✓ sig.
15q13.3 microdeletion syndrome	Congenital exomphalos	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Congenital exomphalos	Currarino syndrome	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Congenital exomphalos	Sacral defect	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Currarino syndrome	Sacral defect	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Neural tube defects, susceptibility to	Yellow nail syndrome	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Caudal regression syndrome	Congenital exomphalos	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Caudal regression syndrome	Currarino syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Neural tube defects, susceptibility to	Sacral defect	0.143	1	6.49e-4	1.22e-3 ✓ sig.
15q13.3 microdeletion syndrome	Congenital omphalocele	0.111	1	9.09e-4	1.56e-3 ✓ sig.
Congenital omphalocele	Sacral defect	0.111	1	9.09e-4	1.56e-3 ✓ sig.
Congenital omphalocele	Currarino syndrome	0.111	1	9.09e-4	1.56e-3 ✓ sig.
autosomal dominant cerebellar ataxia	Vascular brain injury	0.067	1	9.09e-4	1.56e-3 ✓ sig.
Caudal regression syndrome	Congenital omphalocele	0.100	1	1.36e-3	2.13e-3 ✓ sig.
Congenital exomphalos	Vascular brain injury	0.063	1	1.82e-3	2.66e-3 ✓ sig.
Currarino syndrome	Vascular brain injury	0.063	1	1.82e-3	2.66e-3 ✓ sig.
Sacral defect	Vascular brain injury	0.063	1	1.82e-3	2.66e-3 ✓ sig.

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