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Cluster 95

12 diseases · 21 shared-gene connections

12 Diseases

17 Unique genes

0.243 Avg. similarity score

Branchial arch abnormalities syndrome 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.

Branchial arch abnormalities syndrome Branchial cleft anomalies kabuki syndrome 1 Choanal atresia syndrome Vissers-bodmer syndrome Vein of galen aneurysm

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Branchial arch abnormalities syndrome	6	6	1
Branchial cleft anomalies	6	6	1
kabuki syndrome 1	6	6	1
Choanal atresia syndrome	5	5	5
Vissers-bodmer syndrome	5	5	3
Vein of galen aneurysm	4	4	6
Congenital small ears	3	3	5
Burn-mckeown syndrome	2	2	2
choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome	2	2	1
Duane-radial ray syndrome	1	1	2
EPHB4-associated vascular malformation spectrum	1	1	1
holoprosencephaly 12 with or without pancreatic agenesis	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
KMT2D	7 / 12	Branchial arch abnormalities syndrome, Branchial cleft anomalies, Choanal atresia syndrome, Congenital small ears and 3 more
TXNL4A	3 / 12	Burn-mckeown syndrome, Choanal atresia syndrome, choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome
CNOT1	2 / 12	holoprosencephaly 12 with or without pancreatic agenesis, Vissers-bodmer syndrome
EPHB4	2 / 12	EPHB4-associated vascular malformation spectrum, Vein of galen aneurysm
IPO8	2 / 12	Duane-radial ray syndrome, Vissers-bodmer syndrome
POLR1A	2 / 12	Burn-mckeown syndrome, Choanal atresia syndrome

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 ⇵
Breakdown of the nuclear lamina LMNA	Reactome	1 / 3	235×	4.24e-3	3.93e-2 ✓ sig.
Nuclear Envelope Breakdown LMNA	Reactome	1 / 9	78.5×	1.27e-2	7.87e-2
SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion PLXNA3	Reactome	1 / 10	70.6×	1.41e-2	8.38e-2
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation SALL4	Reactome	1 / 13	54.3×	1.83e-2	9.79e-2
Sema3A PAK dependent Axon repulsion PLXNA3	Reactome	1 / 15	47.1×	2.10e-2	1.06e-1
Depolymerisation of the Nuclear Lamina LMNA	Reactome	1 / 15	47.1×	2.10e-2	1.06e-1
CRMPs in Sema3A signaling PLXNA3	Reactome	1 / 16	44.2×	2.24e-2	1.10e-1
Transcriptional regulation of pluripotent stem cells SALL4	Reactome	1 / 17	41.6×	2.38e-2	1.13e-1
Ephrin signaling EPHB4	Reactome	1 / 19	37.2×	2.66e-2	1.21e-1
Initiation of Nuclear Envelope (NE) Reformation LMNA	Reactome	1 / 19	37.2×	2.66e-2	1.21e-1
Axon guidance PLXNA3, EPHB4	KEGG	2 / 183	7.7×	2.70e-2	1.22e-1
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain CNOT1	Reactome	1 / 20	35.3×	2.80e-2	1.24e-1
Interleukin-37 signaling PTPN14	Reactome	1 / 21	33.6×	2.93e-2	1.27e-1
EPH-Ephrin signaling EPHB4	Reactome	1 / 22	32.1×	3.07e-2	1.31e-1
Regulation of TP53 Activity through Acetylation KAT6A	Reactome	1 / 23	30.7×	3.21e-2	1.34e-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 ⇵
heterochromatin formation KMT2D, LMNA, SMARCA2	GO:0031507	3 / 70	47.1×	3.30e-5	1.31e-3 ✓ sig.
cardiac septum morphogenesis CHD7, BMP5	GO:0060411	2 / 16	137×	9.28e-5	2.86e-3 ✓ sig.
pharyngeal system development BMP5, HOXA2	GO:0060037	2 / 21	105×	1.62e-4	4.34e-3 ✓ sig.
motor neuron axon guidance HOXA2, PLXNA3	GO:0008045	2 / 24	91.6×	2.12e-4	5.27e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II KMT2D, CHD7, BMP5, HOXA2, SALL4, SMARCA2	GO:0045944	6 / 1,208	5.5×	4.80e-4	9.31e-3 ✓ sig.
negative regulation of cell population proliferation PTPN14, BMP5, LMNA, SMARCA2	GO:0008285	4 / 444	9.9×	5.85e-4	1.07e-2 ✓ sig.
beta-catenin-TCF complex assembly KMT2D	GO:1904837	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
right ventricular compact myocardium morphogenesis CHD7	GO:0003226	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
rhombomere 3 morphogenesis HOXA2	GO:0021658	1 / 1	1,099×	9.10e-4	1.42e-2 ✓ sig.
tissue development BMP5, SALL4	GO:0009888	2 / 51	43.1×	9.67e-4	1.47e-2 ✓ sig.
cellular senescence LMNA, KAT6A	GO:0090398	2 / 57	38.6×	1.21e-3	1.70e-2 ✓ sig.
pattern specification process BMP5, HOXA2	GO:0007389	2 / 60	36.6×	1.34e-3	1.79e-2 ✓ sig.
heart morphogenesis CHD7, EPHB4	GO:0003007	2 / 61	36.0×	1.38e-3	1.84e-2 ✓ sig.
negative regulation of protein localization to nucleolus POLR1A	GO:1904750	1 / 2	550×	1.82e-3	2.15e-2 ✓ sig.
rhombomere 2 development HOXA2	GO:0021568	1 / 2	550×	1.82e-3	2.15e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Burn-mckeown syndrome	Choanal atresia syndrome	0.333	2	8.44e-8	6.27e-7 ✓ sig.
Branchial arch abnormalities syndrome	kabuki syndrome 1	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Branchial arch abnormalities syndrome	Branchial cleft anomalies	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Branchial cleft anomalies	kabuki syndrome 1	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Burn-mckeown syndrome	choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Branchial cleft anomalies	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Branchial arch abnormalities syndrome	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
holoprosencephaly 12 with or without pancreatic agenesis	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
kabuki syndrome 1	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Branchial arch abnormalities syndrome	Congenital small ears	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Branchial cleft anomalies	Choanal atresia syndrome	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Branchial cleft anomalies	Congenital small ears	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Branchial arch abnormalities syndrome	Choanal atresia syndrome	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Choanal atresia syndrome	kabuki syndrome 1	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Choanal atresia syndrome	choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Congenital small ears	kabuki syndrome 1	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Duane-radial ray syndrome	Vissers-bodmer syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
EPHB4-associated vascular malformation spectrum	Vein of galen aneurysm	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Branchial arch abnormalities syndrome	Vein of galen aneurysm	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Branchial cleft anomalies	Vein of galen aneurysm	0.143	1	3.90e-4	8.52e-4 ✓ sig.
kabuki syndrome 1	Vein of galen aneurysm	0.143	1	3.90e-4	8.52e-4 ✓ sig.

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