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 415

5 diseases · 8 shared-gene connections
5 Diseases
4 Unique genes
0.312 Avg. similarity score
Bestrophinopathy 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 ⇵
Bestrophinopathy 4 4 4
Vitreoretinochoroidopathy 4 4 2
hemochromatosis type 5 3 3 1
neurodegeneration with brain iron accumulation 9 3 3 1
BEST1-related dominant retinopathy 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FTH1 4 / 5 Bestrophinopathy, hemochromatosis type 5, neurodegeneration with brain iron accumulation 9, Vitreoretinochoroidopathy
BEST1 3 / 5 BEST1-related dominant retinopathy, Bestrophinopathy, Vitreoretinochoroidopathy
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 ⇵
Iron uptake and transport
FTH1
 Reactome 1 / 28 107× 9.29e-3 6.56e-2
Ferroptosis
FTH1
 KEGG 1 / 42 71.5× 1.39e-2 8.32e-2
Porphyrin metabolism
FTH1
 KEGG 1 / 46 65.3× 1.52e-2 8.78e-2
Golgi Associated Vesicle Biogenesis
FTH1
 Reactome 1 / 56 53.6× 1.85e-2 9.85e-2
Mineral absorption
FTH1
 KEGG 1 / 61 49.2× 2.02e-2 1.03e-1
Stimuli-sensing channels
BEST1
 Reactome 1 / 79 38.0× 2.61e-2 1.19e-1
Hippo signaling pathway
CRB1
 KEGG 1 / 157 19.1× 5.13e-2 1.74e-1
Necroptosis
FTH1
 KEGG 1 / 159 18.9× 5.19e-2 1.75e-1
Neutrophil degranulation
FTH1
 Reactome 1 / 480 6.3× 1.51e-1 3.10e-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 ⇵
detection of light stimulus involved in visual perception
BEST1, CRB1, PRPH2
 GO:0050908 3 / 24 584× 7.44e-9 1.32e-6 ✓ sig.
photoreceptor cell outer segment organization
CRB1, PRPH2
 GO:0035845 2 / 15 623× 3.61e-6 2.31e-4 ✓ sig.
visual perception
BEST1, CRB1, PRPH2
 GO:0007601 3 / 215 65.2× 5.96e-6 3.45e-4 ✓ sig.
retina development in camera-type eye
CRB1, PRPH2
 GO:0060041 2 / 85 110× 1.22e-4 3.51e-3 ✓ sig.
response to low light intensity stimulus
PRPH2
 GO:0009645 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
gamma-aminobutyric acid secretion, neurotransmission
BEST1
 GO:0061534 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
post-embryonic retina morphogenesis in camera-type eye
CRB1
 GO:0060060 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
establishment of bipolar cell polarity involved in cell morphogenesis
CRB1
 GO:0061159 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
transepithelial chloride transport
BEST1
 GO:0030321 1 / 9 519× 1.93e-3 2.20e-2 ✓ sig.
glutamate secretion
BEST1
 GO:0014047 1 / 11 425× 2.35e-3 2.48e-2 ✓ sig.
negative regulation of ferroptosis
FTH1
 GO:0110076 1 / 14 334× 2.99e-3 2.82e-2 ✓ sig.
retina morphogenesis in camera-type eye
CRB1
 GO:0060042 1 / 14 334× 2.99e-3 2.82e-2 ✓ sig.
protein heterooligomerization
PRPH2
 GO:0051291 1 / 15 311× 3.21e-3 2.91e-2 ✓ sig.
cellular response to light stimulus
CRB1
 GO:0071482 1 / 16 292× 3.42e-3 3.03e-2 ✓ sig.
plasma membrane organization
CRB1
 GO:0007009 1 / 21 222× 4.49e-3 3.47e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bestrophinopathy Vitreoretinochoroidopathy 0.400 2 5.06e-8 3.92e-7 ✓ sig.
hemochromatosis type 5 neurodegeneration with brain iron accumulation 9 0.500 1 6.49e-5 2.34e-4 ✓ sig.
BEST1-related dominant retinopathy Vitreoretinochoroidopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
hemochromatosis type 5 Vitreoretinochoroidopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
neurodegeneration with brain iron accumulation 9 Vitreoretinochoroidopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
BEST1-related dominant retinopathy Bestrophinopathy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bestrophinopathy hemochromatosis type 5 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bestrophinopathy neurodegeneration with brain iron accumulation 9 0.200 1 2.60e-4 6.40e-4 ✓ sig.