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 298

6 diseases · 9 shared-gene connections
6 Diseases
37 Unique genes
0.098 Avg. similarity score
Congenital hydrocephalus Most-connected disease (5 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Congenital hydrocephalus 5 5 14
Hydrocephalus 4 4 26
Congenital communicating hydrocephalus 3 3 3
Cryptospermia 3 3 4
SMARCC1-associated developmental dysgenesis syndrome 2 2 1
scott syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TRIM71 4 / 6 Congenital communicating hydrocephalus, Congenital hydrocephalus, Cryptospermia, Hydrocephalus
MPDZ 3 / 6 Congenital communicating hydrocephalus, Congenital hydrocephalus, Hydrocephalus
SMARCC1 3 / 6 Congenital hydrocephalus, Hydrocephalus, SMARCC1-associated developmental dysgenesis syndrome
WDR81 3 / 6 Congenital communicating hydrocephalus, Congenital hydrocephalus, Hydrocephalus
ANO6 2 / 6 Congenital hydrocephalus, scott syndrome
CCDC88C 2 / 6 Congenital hydrocephalus, Hydrocephalus
L1CAM 2 / 6 Congenital hydrocephalus, Hydrocephalus
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 ⇵
Mannose type O-glycan biosynthesis
CRPPA, POMGNT1
 KEGG 2 / 23 28.2× 2.24e-3 2.48e-2 ✓ sig.
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 325× 3.08e-3 3.13e-2 ✓ sig.
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 325× 3.08e-3 3.13e-2 ✓ sig.
Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3
POMGNT1
 Reactome 1 / 2 162× 6.15e-3 5.02e-2
Recycling pathway of L1
KIF4A, L1CAM
 Reactome 2 / 40 16.2× 6.69e-3 5.30e-2
Loss of MECP2 binding ability to 5mC-DNA
SIN3A
 Reactome 1 / 3 108× 9.21e-3 6.53e-2
L1CAM interactions
L1CAM
 Reactome 1 / 4 81.1× 1.23e-2 7.74e-2
Hedgehog signaling pathway
PTCH1, CCND2
 KEGG 2 / 56 11.6× 1.28e-2 7.92e-2
Hedgehog 'off' state
PTCH1, IFT122
 Reactome 2 / 56 11.6× 1.28e-2 7.92e-2
MicroRNAs in cancer
TRIM71, CCND2, FZD3, PDGFRB
 KEGG 4 / 311 4.2× 1.49e-2 8.66e-2
Beta oxidation of octanoyl-CoA to hexanoyl-CoA
ACADM
 Reactome 1 / 5 64.9× 1.53e-2 8.81e-2
Basal cell carcinoma
PTCH1, FZD3
 KEGG 2 / 63 10.3× 1.60e-2 9.07e-2
Wnt signaling pathway
CCDC88C, CCND2, FZD3
 KEGG 3 / 174 5.6× 1.62e-2 9.12e-2
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids
ACADM
 Reactome 1 / 6 54.1× 1.83e-2 9.81e-2
Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA
ACADM
 Reactome 1 / 6 54.1× 1.83e-2 9.81e-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 ⇵
neural tube closure
TRIM71, PTCH1, FZD3, IFT122
 GO:0001843 4 / 85 23.8× 2.35e-5 1.01e-3 ✓ sig.
cilium movement
CCDC88C, DNAH9, HYDIN
 GO:0003341 3 / 48 31.6× 1.16e-4 3.39e-3 ✓ sig.
animal organ morphogenesis
PTCH1, SMARCC1, SYCP2, FGFR2
 GO:0009887 4 / 130 15.5× 1.24e-4 3.55e-3 ✓ sig.
mucociliary clearance
CCDC88C, DNAH9
 GO:0120197 2 / 12 84.2× 2.49e-4 5.90e-3 ✓ sig.
commissural neuron axon guidance
PTCH1, FZD3
 GO:0071679 2 / 14 72.2× 3.42e-4 7.34e-3 ✓ sig.
prostate gland development
PTCH1, SMARCC1
 GO:0030850 2 / 16 63.1× 4.50e-4 8.90e-3 ✓ sig.
protein O-linked glycosylation via mannose
CRPPA, POMGNT1
 GO:0035269 2 / 18 56.1× 5.72e-4 1.05e-2 ✓ sig.
female gamete generation
DMC1, M1AP
 GO:0007292 2 / 21 48.1× 7.82e-4 1.29e-2 ✓ sig.
negative regulation of keratinocyte proliferation
PTCH1, FGFR2
 GO:0010839 2 / 24 42.1× 1.02e-3 1.53e-2 ✓ sig.
basement membrane organization
NID1, POMGNT1
 GO:0071711 2 / 29 34.8× 1.50e-3 1.91e-2 ✓ sig.
regulation of smoothened signaling pathway
PTCH1, FGFR2
 GO:0008589 2 / 29 34.8× 1.50e-3 1.91e-2 ✓ sig.
non-canonical Wnt signaling pathway
CCDC88C, FZD3
 GO:0035567 2 / 33 30.6× 1.94e-3 2.21e-2 ✓ sig.
response to methylglyoxal
SIN3A
 GO:0051595 1 / 1 505× 1.98e-3 2.24e-2 ✓ sig.
cellular response to tert-butyl hydroperoxide
SIN3A
 GO:0072736 1 / 1 505× 1.98e-3 2.24e-2 ✓ sig.
phosphatidylserine exposure on blood platelet
ANO6
 GO:0097045 1 / 1 505× 1.98e-3 2.24e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital hydrocephalus Hydrocephalus 0.171 6 3.71e-14 5.24e-13 ✓ sig.
Congenital communicating hydrocephalus Congenital hydrocephalus 0.200 3 5.98e-10 5.84e-9 ✓ sig.
Congenital communicating hydrocephalus Hydrocephalus 0.111 3 4.27e-9 3.84e-8 ✓ sig.
Congenital communicating hydrocephalus Cryptospermia 0.143 1 7.79e-4 1.39e-3 ✓ sig.
Congenital hydrocephalus SMARCC1-associated developmental dysgenesis syndrome 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Congenital hydrocephalus scott syndrome 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Hydrocephalus SMARCC1-associated developmental dysgenesis syndrome 0.037 1 1.69e-3 2.51e-3 ✓ sig.
Congenital hydrocephalus Cryptospermia 0.056 1 3.63e-3 4.66e-3 ✓ sig.
Cryptospermia Hydrocephalus 0.033 1 6.74e-3 8.02e-3 ✓ sig.