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 385

5 diseases · 10 shared-gene connections
5 Diseases
2 Unique genes
0.417 Avg. similarity score
Ciliary dyskinesia with retinitis pigmentosa 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 ⇵
Ciliary dyskinesia with retinitis pigmentosa 4 4 1
Cone-rod dystrophy, x-linked 4 4 2
RPGR-related retinopathy 4 4 1
Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness 4 4 1
X-linked cone-rod dystrophy 4 4 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
RPGR 5 / 5 Ciliary dyskinesia with retinitis pigmentosa, Cone-rod dystrophy, x-linked, Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness, RPGR-related retinopathy and 1 more
CACNA1F 2 / 5 Cone-rod dystrophy, x-linked, X-linked cone-rod dystrophy
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 ⇵
Phase 2 - plateau phase
CACNA1F
 Reactome 1 / 25 240× 4.16e-3 3.87e-2 ✓ sig.
Phase 0 - rapid depolarisation
CACNA1F
 Reactome 1 / 44 136× 7.31e-3 5.62e-2
Cortisol synthesis and secretion
CACNA1F
 KEGG 1 / 65 92.4× 1.08e-2 7.19e-2
GnRH secretion
CACNA1F
 KEGG 1 / 65 92.4× 1.08e-2 7.19e-2
Renin secretion
CACNA1F
 KEGG 1 / 69 87.0× 1.15e-2 7.45e-2
Insulin secretion
CACNA1F
 KEGG 1 / 86 69.8× 1.43e-2 8.46e-2
Arrhythmogenic right ventricular cardiomyopathy
CACNA1F
 KEGG 1 / 86 69.8× 1.43e-2 8.46e-2
Cardiac muscle contraction
CACNA1F
 KEGG 1 / 87 69.0× 1.44e-2 8.52e-2
GABAergic synapse
CACNA1F
 KEGG 1 / 89 67.5× 1.48e-2 8.63e-2
GnRH signaling pathway
CACNA1F
 KEGG 1 / 93 64.6× 1.54e-2 8.85e-2
Aldosterone synthesis and secretion
CACNA1F
 KEGG 1 / 98 61.3× 1.63e-2 9.14e-2
Hypertrophic cardiomyopathy
CACNA1F
 KEGG 1 / 99 60.7× 1.64e-2 9.18e-2
Dilated cardiomyopathy
CACNA1F
 KEGG 1 / 105 57.2× 1.74e-2 9.52e-2
Cholinergic synapse
CACNA1F
 KEGG 1 / 115 52.2× 1.91e-2 1.00e-1
Serotonergic synapse
CACNA1F
 KEGG 1 / 115 52.2× 1.91e-2 1.00e-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 ⇵
visual perception
RPGR, CACNA1F
 GO:0007601 2 / 215 86.9× 1.32e-4 3.72e-3 ✓ sig.
protein localization to non-motile cilium
RPGR
 GO:0097499 1 / 4 2,336× 4.28e-4 8.59e-3 ✓ sig.
negative regulation of voltage-gated calcium channel activity
CACNA1F
 GO:1901386 1 / 6 1,557× 6.42e-4 1.13e-2 ✓ sig.
eye photoreceptor cell development
RPGR
 GO:0042462 1 / 21 445× 2.25e-3 2.41e-2 ✓ sig.
detection of light stimulus involved in visual perception
CACNA1F
 GO:0050908 1 / 24 389× 2.57e-3 2.58e-2 ✓ sig.
calcium ion import across plasma membrane
CACNA1F
 GO:0098703 1 / 28 334× 2.99e-3 2.82e-2 ✓ sig.
intraciliary transport
RPGR
 GO:0042073 1 / 36 260× 3.85e-3 3.22e-2 ✓ sig.
cilium organization
RPGR
 GO:0044782 1 / 40 234× 4.28e-3 3.38e-2 ✓ sig.
positive regulation of autophagy
RPGR
 GO:0010508 1 / 92 102× 9.82e-3 5.08e-2
calcium ion transmembrane transport
CACNA1F
 GO:0070588 1 / 149 62.7× 1.59e-2 6.41e-2
calcium ion transport
CACNA1F
 GO:0006816 1 / 157 59.5× 1.67e-2 6.57e-2
cell projection organization
RPGR
 GO:0030030 1 / 214 43.7× 2.28e-2 7.69e-2
cilium assembly
RPGR
 GO:0060271 1 / 237 39.4× 2.52e-2 8.09e-2
ubiquitin-dependent protein catabolic process
RPGR
 GO:0006511 1 / 257 36.4× 2.73e-2 8.40e-2
intracellular protein transport
RPGR
 GO:0006886 1 / 279 33.5× 2.96e-2 8.71e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cone-rod dystrophy, x-linked X-linked cone-rod dystrophy 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Ciliary dyskinesia with retinitis pigmentosa Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ciliary dyskinesia with retinitis pigmentosa RPGR-related retinopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness RPGR-related retinopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ciliary dyskinesia with retinitis pigmentosa Cone-rod dystrophy, x-linked 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ciliary dyskinesia with retinitis pigmentosa X-linked cone-rod dystrophy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cone-rod dystrophy, x-linked Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Retinitis pigmentosa, x-linked, and sinorespiratory infections with or without deafness X-linked cone-rod dystrophy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cone-rod dystrophy, x-linked RPGR-related retinopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
RPGR-related retinopathy X-linked cone-rod dystrophy 0.333 1 1.30e-4 3.90e-4 ✓ sig.