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Cluster 144

9 diseases · 12 shared-gene connections

9 Diseases

13 Unique genes

0.223 Avg. similarity score

Vissers-bodmer syndrome Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: holoprosencephaly 12 with or without pancreatic agenesis 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.

holoprosencephaly 12 with or without pancreatic agenesis Vissers-bodmer syndrome Branchial arch abnormalities syndrome Branchial cleft anomalies Choanal atresia syndrome Vein of galen aneurysm

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Vissers-bodmer syndrome	5	5	3
Branchial arch abnormalities syndrome	4	4	1
Branchial cleft anomalies	4	4	1
Choanal atresia syndrome	4	4	5
Vein of galen aneurysm	3	3	6
Burn-mckeown syndrome	1	1	2
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	5 / 9	Branchial arch abnormalities syndrome, Branchial cleft anomalies, Choanal atresia syndrome, Vein of galen aneurysm and 1 more
CNOT1	2 / 9	holoprosencephaly 12 with or without pancreatic agenesis, Vissers-bodmer syndrome
EPHB4	2 / 9	EPHB4-associated vascular malformation spectrum, Vein of galen aneurysm
IPO8	2 / 9	Duane-radial ray syndrome, Vissers-bodmer syndrome
POLR1A	2 / 9	Burn-mckeown syndrome, Choanal atresia syndrome
TXNL4A	2 / 9	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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation SALL4	Reactome	1 / 13	71.1×	1.40e-2	8.67e-2
Transcriptional regulation of pluripotent stem cells SALL4	Reactome	1 / 17	54.3×	1.83e-2	1.02e-1
Ephrin signaling EPHB4	Reactome	1 / 19	48.6×	2.04e-2	1.08e-1
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain CNOT1	Reactome	1 / 20	46.2×	2.14e-2	1.11e-1
Interleukin-37 signaling PTPN14	Reactome	1 / 21	44.0×	2.25e-2	1.14e-1
EPH-Ephrin signaling EPHB4	Reactome	1 / 22	42.0×	2.36e-2	1.18e-1
Regulation of TP53 Activity through Acetylation KAT6A	Reactome	1 / 23	40.2×	2.46e-2	1.21e-1
Deadenylation of mRNA CNOT1	Reactome	1 / 24	38.5×	2.57e-2	1.23e-1
RNA Polymerase I Transcription Termination POLR1A	Reactome	1 / 32	28.9×	3.41e-2	1.44e-1
RNA polymerase POLR1A	KEGG	1 / 34	27.2×	3.62e-2	1.48e-1
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known SMARCA2	Reactome	1 / 38	24.3×	4.04e-2	1.57e-1
EPHB-mediated forward signaling EPHB4	Reactome	1 / 39	23.7×	4.14e-2	1.59e-1
Deactivation of the beta-catenin transactivating complex KMT2D	Reactome	1 / 42	22.0×	4.45e-2	1.66e-1
RNA Polymerase I Transcription Initiation POLR1A	Reactome	1 / 45	20.5×	4.77e-2	1.72e-1
Virion - Hepatitis viruses CLDN14	KEGG	1 / 48	19.2×	5.08e-2	1.78e-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 ⇵
right ventricular compact myocardium morphogenesis CHD7	GO:0003226	1 / 1	1,437×	6.96e-4	1.23e-2 ✓ sig.
beta-catenin-TCF complex assembly KMT2D	GO:1904837	1 / 1	1,437×	6.96e-4	1.23e-2 ✓ sig.
heart morphogenesis CHD7, EPHB4	GO:0003007	2 / 61	47.1×	7.99e-4	1.35e-2 ✓ sig.
heterochromatin formation KMT2D, SMARCA2	GO:0031507	2 / 70	41.1×	1.05e-3	1.61e-2 ✓ sig.
negative regulation of protein localization to nucleolus POLR1A	GO:1904750	1 / 2	719×	1.39e-3	1.90e-2 ✓ sig.
regulation of growth hormone secretion CHD7	GO:0060123	1 / 3	479×	2.09e-3	2.39e-2 ✓ sig.
olfactory nerve development CHD7	GO:0021553	1 / 3	479×	2.09e-3	2.39e-2 ✓ sig.
cranial nerve development CHD7	GO:0021545	1 / 4	359×	2.78e-3	2.80e-2 ✓ sig.
oocyte growth KMT2D	GO:0001555	1 / 4	359×	2.78e-3	2.80e-2 ✓ sig.
nucleolar large rRNA transcription by RNA polymerase I POLR1A	GO:0042790	1 / 4	359×	2.78e-3	2.80e-2 ✓ sig.
chromatin organization KMT2D, CHD7, KAT6A	GO:0006325	3 / 449	9.6×	3.29e-3	3.08e-2 ✓ sig.
ear morphogenesis CHD7	GO:0042471	1 / 5	287×	3.47e-3	3.15e-2 ✓ sig.
regulation of axon diameter KEL	GO:0031133	1 / 5	287×	3.47e-3	3.15e-2 ✓ sig.
intracellular magnesium ion homeostasis KEL	GO:0010961	1 / 6	240×	4.17e-3	3.45e-2 ✓ sig.
positive regulation of cytoplasmic mRNA processing body assembly CNOT1	GO:0010606	1 / 6	240×	4.17e-3	3.45e-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	5.94e-7 ✓ sig.
Branchial arch abnormalities syndrome	Branchial cleft anomalies	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Branchial arch abnormalities syndrome	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Branchial cleft anomalies	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.35e-4 ✓ sig.
holoprosencephaly 12 with or without pancreatic agenesis	Vissers-bodmer syndrome	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Branchial arch abnormalities syndrome	Choanal atresia syndrome	0.167	1	3.25e-4	7.71e-4 ✓ sig.
Branchial cleft anomalies	Choanal atresia syndrome	0.167	1	3.25e-4	7.71e-4 ✓ sig.
Duane-radial ray syndrome	Vissers-bodmer syndrome	0.200	1	3.90e-4	8.67e-4 ✓ sig.
Branchial arch abnormalities syndrome	Vein of galen aneurysm	0.143	1	3.90e-4	8.67e-4 ✓ sig.
Branchial cleft anomalies	Vein of galen aneurysm	0.143	1	3.90e-4	8.67e-4 ✓ sig.
EPHB4-associated vascular malformation spectrum	Vein of galen aneurysm	0.143	1	3.90e-4	8.67e-4 ✓ sig.
Choanal atresia syndrome	Vissers-bodmer syndrome	0.125	1	9.74e-4	1.67e-3 ✓ sig.

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