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Cluster 453

6 diseases · 8 shared-gene connections

6 Diseases

16 Unique genes

0.224 Avg. similarity score

Dental enamel hypoplasia Most-connected disease (5 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.

Dental enamel hypoplasia Intellectual disability and central nervous system anomalies Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies Testicular regression syndrome Baker-gordon syndrome Pycnodysostosis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Dental enamel hypoplasia	5	5	16
Intellectual disability and central nervous system anomalies	3	3	1
Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies	3	3	1
Testicular regression syndrome	3	3	1
Baker-gordon syndrome	1	1	1
Pycnodysostosis	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
DHX37	4 / 6	Dental enamel hypoplasia, Intellectual disability and central nervous system anomalies, Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies, Testicular regression syndrome
CTSK	2 / 6	Dental enamel hypoplasia, Pycnodysostosis
SYT1	2 / 6	Baker-gordon syndrome, Dental enamel hypoplasia

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 SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) SLC4A4	Reactome	1 / 1	751×	1.33e-3	1.41e-2 ✓ sig.
Toxicity of botulinum toxin type B (BoNT/B) SYT1	Reactome	1 / 3	250×	3.99e-3	3.12e-2 ✓ sig.
SMAD4 MH2 Domain Mutants in Cancer SMAD2	Reactome	1 / 3	250×	3.99e-3	3.12e-2 ✓ sig.
SMAD2/3 MH2 Domain Mutants in Cancer SMAD2	Reactome	1 / 3	250×	3.99e-3	3.12e-2 ✓ sig.
Regulation of commissural axon pathfinding by SLIT and ROBO ROBO1	Reactome	1 / 3	250×	3.99e-3	3.12e-2 ✓ sig.
Toxicity of botulinum toxin type G (BoNT/G) SYT1	Reactome	1 / 3	250×	3.99e-3	3.12e-2 ✓ sig.
Role of ABL in ROBO-SLIT signaling ROBO1	Reactome	1 / 4	188×	5.32e-3	3.80e-2 ✓ sig.
SLIT2:ROBO1 increases RHOA activity ROBO1	Reactome	1 / 4	188×	5.32e-3	3.80e-2 ✓ sig.
Signaling by NODAL SMAD2	Reactome	1 / 6	125×	7.97e-3	4.94e-2 ✓ sig.
RUNX1 regulates transcription of genes involved in differentiation of keratinocytes CTSK	Reactome	1 / 6	125×	7.97e-3	4.94e-2 ✓ sig.
SMAD2/3 Phosphorylation Motif Mutants in Cancer SMAD2	Reactome	1 / 6	125×	7.97e-3	4.94e-2 ✓ sig.
TGFBR1 KD Mutants in Cancer SMAD2	Reactome	1 / 6	125×	7.97e-3	4.94e-2 ✓ sig.
Regulation of expression of SLITs and ROBOs ROBO1	Reactome	1 / 8	93.8×	1.06e-2	5.90e-2
Bicarbonate transporters SLC4A4	Reactome	1 / 10	75.1×	1.32e-2	6.74e-2
FOXO-mediated transcription of cell cycle genes SMAD2	Reactome	1 / 11	68.2×	1.46e-2	7.13e-2

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

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
pulmonary valve morphogenesis ROBO1, SMAD2	GO:0003184	2 / 18	130×	1.04e-4	3.19e-3 ✓ sig.
SMAD protein signal transduction SMAD2, ZMIZ1	GO:0060395	2 / 25	93.4×	2.04e-4	5.16e-3 ✓ sig.
outflow tract septum morphogenesis MSX2, ROBO1	GO:0003148	2 / 28	83.4×	2.56e-4	6.06e-3 ✓ sig.
developmental growth SMAD2, ZMIZ1	GO:0048589	2 / 30	77.9×	2.95e-4	6.69e-3 ✓ sig.
aortic valve morphogenesis ROBO1, SMAD2	GO:0003180	2 / 37	63.1×	4.50e-4	8.85e-3 ✓ sig.
positive regulation of BMP signaling pathway MSX2, SMAD2	GO:0030513	2 / 40	58.4×	5.26e-4	9.86e-3 ✓ sig.
positive regulation of Notch signaling pathway ROBO1, ZMIZ1	GO:0045747	2 / 50	46.7×	8.22e-4	1.31e-2 ✓ sig.
synchronous neurotransmitter secretion SYT1	GO:0071911	1 / 1	1,168×	8.56e-4	1.33e-2 ✓ sig.
fast, calcium ion-dependent exocytosis of neurotransmitter SYT1	GO:0098746	1 / 1	1,168×	8.56e-4	1.33e-2 ✓ sig.
brain development DHX37, MACROD2, ROBO1	GO:0007420	3 / 244	14.4×	1.09e-3	1.53e-2 ✓ sig.
cell surface receptor signaling pathway involved in heart development MSX2	GO:0061311	1 / 2	584×	1.71e-3	1.96e-2 ✓ sig.
chemorepulsion involved in postnatal olfactory bulb interneuron migration ROBO1	GO:0021836	1 / 2	584×	1.71e-3	1.96e-2 ✓ sig.
pyramidal neuron migration to cerebral cortex ZMIZ1	GO:0021852	1 / 3	389×	2.57e-3	2.40e-2 ✓ sig.
frontal suture morphogenesis MSX2	GO:0060364	1 / 3	389×	2.57e-3	2.40e-2 ✓ sig.
purine nucleoside metabolic process MACROD2	GO:0042278	1 / 3	389×	2.57e-3	2.40e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Intellectual disability and central nervous system anomalies	Testicular regression syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual disability and central nervous system anomalies	Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies	Testicular regression syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Baker-gordon syndrome	Dental enamel hypoplasia	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Dental enamel hypoplasia	Testicular regression syndrome	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Dental enamel hypoplasia	Intellectual disability and central nervous system anomalies	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Dental enamel hypoplasia	Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies	0.059	1	1.03e-3	1.57e-3 ✓ sig.
Dental enamel hypoplasia	Pycnodysostosis	0.059	1	1.03e-3	1.57e-3 ✓ sig.

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