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 477

6 diseases · 8 shared-gene connections
6 Diseases
8 Unique genes
0.236 Avg. similarity score
Caudal regression syndrome Most-connected disease (4 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 ⇵
Caudal regression syndrome 4 4 3
Neural tube defects, susceptibility to 4 4 5
Sacral defect 3 3 2
Currarino syndrome 2 2 2
Skeletal ciliopathy 2 2 2
Yellow nail syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FUZ 3 / 6 Caudal regression syndrome, Neural tube defects, susceptibility to, Skeletal ciliopathy
PCSK5 3 / 6 Caudal regression syndrome, Currarino syndrome, Sacral defect
VANGL1 3 / 6 Caudal regression syndrome, Neural tube defects, susceptibility to, Sacral defect
CELSR1 2 / 6 Neural tube defects, susceptibility to, Yellow nail 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 ⇵
Hedgehog 'off' state
FUZ, INTU
 Reactome 2 / 56 53.6× 5.87e-4 7.56e-3 ✓ sig.
NGF processing
PCSK5
 Reactome 1 / 4 375× 2.66e-3 2.34e-2 ✓ sig.
Wnt signaling pathway
VANGL1, VANGL2
 KEGG 2 / 174 17.3× 5.52e-3 3.89e-2 ✓ sig.
Assembly of active LPL and LIPC lipase complexes
PCSK5
 Reactome 1 / 11 136× 7.31e-3 4.67e-2 ✓ sig.
Maturity onset diabetes of the young
MNX1
 KEGG 1 / 26 57.7× 1.72e-2 7.86e-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 ⇵
establishment of planar polarity
FUZ, CELSR1, VANGL2, INTU
 GO:0001736 4 / 16 584× 2.50e-11 8.74e-9 ✓ sig.
orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis
CELSR1, VANGL2
 GO:0060488 2 / 2 2,336× 1.60e-7 1.89e-5 ✓ sig.
planar dichotomous subdivision of terminal units involved in lung branching morphogenesis
CELSR1, VANGL2
 GO:0060489 2 / 2 2,336× 1.60e-7 1.89e-5 ✓ sig.
lateral sprouting involved in lung morphogenesis
CELSR1, VANGL2
 GO:0060490 2 / 2 2,336× 1.60e-7 1.89e-5 ✓ sig.
Wnt signaling pathway, planar cell polarity pathway
VANGL1, CELSR1, VANGL2
 GO:0060071 3 / 34 206× 3.06e-7 3.24e-5 ✓ sig.
establishment of body hair planar orientation
CELSR1, VANGL2
 GO:0048105 2 / 4 1,168× 9.62e-7 8.33e-5 ✓ sig.
non-motile cilium assembly
FUZ, VANGL2, INTU
 GO:1905515 3 / 57 123× 1.49e-6 1.20e-4 ✓ sig.
neural tube closure
FUZ, CELSR1, VANGL2
 GO:0001843 3 / 85 82.4× 5.00e-6 3.18e-4 ✓ sig.
apical protein localization
CELSR1, VANGL2
 GO:0045176 2 / 16 292× 1.92e-5 8.97e-4 ✓ sig.
regulation of smoothened signaling pathway
FUZ, INTU
 GO:0008589 2 / 29 161× 6.47e-5 2.24e-3 ✓ sig.
intraciliary transport
FUZ, INTU
 GO:0042073 2 / 36 130× 1.00e-4 3.10e-3 ✓ sig.
neural tube development
FUZ, INTU
 GO:0021915 2 / 45 104× 1.57e-4 4.29e-3 ✓ sig.
hair follicle development
FUZ, VANGL2
 GO:0001942 2 / 48 97.3× 1.79e-4 4.70e-3 ✓ sig.
regulation of cilium assembly
FUZ, INTU
 GO:1902017 2 / 52 89.8× 2.10e-4 5.27e-3 ✓ sig.
Rho protein signal transduction
CELSR1, VANGL2
 GO:0007266 2 / 66 70.8× 3.39e-4 7.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Caudal regression syndrome Sacral defect 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Caudal regression syndrome Neural tube defects, susceptibility to 0.286 2 2.50e-7 1.65e-6 ✓ sig.
Currarino syndrome Sacral defect 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Neural tube defects, susceptibility to Yellow nail syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Caudal regression syndrome Currarino syndrome 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Caudal regression syndrome Skeletal ciliopathy 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Neural tube defects, susceptibility to Skeletal ciliopathy 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Neural tube defects, susceptibility to Sacral defect 0.143 1 6.46e-4 1.09e-3 ✓ sig.