Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 345

7 diseases · 11 shared-gene connections
7 Diseases
10 Unique genes
0.255 Avg. similarity score
Anodontia Most-connected disease (4 links)
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Disease Searched: Hamamy syndrome 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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Anodontia 4 4 4
Craniofacial dysplasia - osteopenia syndrome 4 4 1
Frontonasal dysplasia 4 4 7
Hamamy syndrome 4 4 1
Hypertelorism, severe, with midface prominence, myopia, intellectual developmental disorder, and bone fragility 4 4 1
Frontonasal dysplasia, severe microphthalmia, severe facial clefting syndrome 1 1 1
Severe neonatal spondylometaphyseal dysplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IRX5 5 / 7 Anodontia, Craniofacial dysplasia - osteopenia syndrome, Frontonasal dysplasia, Hamamy syndrome and 1 more
ALX1 2 / 7 Frontonasal dysplasia, Frontonasal dysplasia, severe microphthalmia, severe facial clefting syndrome
SBDS 2 / 7 Anodontia, Severe neonatal spondylometaphyseal dysplasia
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 ⇵
Ephrin signaling
EFNB1
 Reactome 1 / 19 63.2× 1.57e-2 7.46e-2
EPH-Ephrin signaling
EFNB1
 Reactome 1 / 22 54.6× 1.82e-2 8.11e-2
Molecules associated with elastic fibres
LTBP3
 Reactome 1 / 38 31.6× 3.12e-2 1.11e-1
EPHB-mediated forward signaling
EFNB1
 Reactome 1 / 39 30.8× 3.20e-2 1.12e-1
EPH-ephrin mediated repulsion of cells
EFNB1
 Reactome 1 / 50 24.0× 4.09e-2 1.29e-1
Ribosome biogenesis in eukaryotes
SBDS
 KEGG 1 / 125 9.6× 9.94e-2 2.16e-1
Axon guidance
EFNB1
 KEGG 1 / 183 6.6× 1.42e-1 2.67e-1
Human T-cell leukemia virus 1 infection
MSX1
 KEGG 1 / 224 5.4× 1.72e-1 3.01e-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 ⇵
embryonic skeletal system morphogenesis
ALX1, ALX3, ALX4, SIX2
 GO:0048704 4 / 53 141× 1.20e-8 2.06e-6 ✓ sig.
embryonic hindlimb morphogenesis
MSX1, ALX3, ALX4
 GO:0035116 3 / 29 193× 4.00e-7 4.04e-5 ✓ sig.
embryonic forelimb morphogenesis
MSX1, ALX3, ALX4
 GO:0035115 3 / 33 170× 5.97e-7 5.65e-5 ✓ sig.
roof of mouth development
MSX1, ALX1, ALX4
 GO:0060021 3 / 70 80.1× 5.93e-6 3.63e-4 ✓ sig.
neuron development
ALX1, ALX3, ALX4
 GO:0048666 3 / 77 72.8× 7.91e-6 4.55e-4 ✓ sig.
anterior/posterior pattern specification
MSX1, ALX1, ALX4
 GO:0009952 3 / 112 50.1× 2.44e-5 1.07e-3 ✓ sig.
regulation of DNA-templated transcription
IRX5, MSX1, ALX1, ALX3, ALX4, SIX2
 GO:0006355 6 / 1,454 7.7× 3.51e-5 1.41e-3 ✓ sig.
middle ear morphogenesis
MSX1, SIX2
 GO:0042474 2 / 22 170× 5.92e-5 2.10e-3 ✓ sig.
embryonic cranial skeleton morphogenesis
IRX5, SIX2
 GO:0048701 2 / 31 121× 1.19e-4 3.50e-3 ✓ sig.
bone morphogenesis
LTBP3, MSX1
 GO:0060349 2 / 32 117× 1.27e-4 3.66e-3 ✓ sig.
bone mineralization
LTBP3, SBDS
 GO:0030282 2 / 56 66.7× 3.91e-4 8.05e-3 ✓ sig.
embryonic digit morphogenesis
MSX1, ALX4
 GO:0042733 2 / 57 65.6× 4.05e-4 8.24e-3 ✓ sig.
embryonic limb morphogenesis
MSX1, ALX1
 GO:0030326 2 / 59 63.3× 4.34e-4 8.63e-3 ✓ sig.
pattern specification process
ALX3, ALX4
 GO:0007389 2 / 60 62.3× 4.49e-4 8.83e-3 ✓ sig.
chondrocyte differentiation
LTBP3, SIX2
 GO:0002062 2 / 61 61.3× 4.64e-4 9.05e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Craniofacial dysplasia - osteopenia syndrome Hypertelorism, severe, with midface prominence, myopia, intellectual developmental disorder, and bone fragility 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Craniofacial dysplasia - osteopenia syndrome Hamamy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hamamy syndrome Hypertelorism, severe, with midface prominence, myopia, intellectual developmental disorder, and bone fragility 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Anodontia Severe neonatal spondylometaphyseal dysplasia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Anodontia Craniofacial dysplasia - osteopenia syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Anodontia Hypertelorism, severe, with midface prominence, myopia, intellectual developmental disorder, and bone fragility 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Anodontia Hamamy syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Craniofacial dysplasia - osteopenia syndrome Frontonasal dysplasia 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Frontonasal dysplasia Hypertelorism, severe, with midface prominence, myopia, intellectual developmental disorder, and bone fragility 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Frontonasal dysplasia Hamamy syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Frontonasal dysplasia Frontonasal dysplasia, severe microphthalmia, severe facial clefting syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.