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 462

6 diseases · 11 shared-gene connections
6 Diseases
3 Unique genes
0.386 Avg. similarity score
Blue cone monochromatism 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 ⇵
Blue cone monochromatism 5 5 3
Colorblindness, partial, protan series 4 4 1
Cone monochromatism 4 4 2
Red color blindness 4 4 1
X-linked cone dysfunction syndrome with myopia 4 4 2
Tritan color blindness 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
OPN1LW 5 / 6 Blue cone monochromatism, Colorblindness, partial, protan series, Cone monochromatism, Red color blindness and 1 more
OPN1MW 3 / 6 Blue cone monochromatism, Cone monochromatism, X-linked cone dysfunction syndrome with myopia
OPN1SW 2 / 6 Blue cone monochromatism, Tritan color blindness
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 ⇵
The retinoid cycle in cones (daylight vision)
OPN1SW, OPN1MW
 Reactome 2 / 8 1,001× 1.16e-6 4.77e-5 ✓ sig.
Opsins
OPN1SW, OPN1MW
 Reactome 2 / 10 801× 1.87e-6 7.16e-5 ✓ sig.
Retinoid cycle disease events
OPN1SW, OPN1MW
 Reactome 2 / 13 616× 3.24e-6 1.14e-4 ✓ sig.
G alpha (i) signalling events
OPN1SW, OPN1MW
 Reactome 2 / 249 32.2× 1.27e-3 1.36e-2 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
absorption of visible light
OPN1SW, OPN1LW, OPN1MW
 GO:0016038 3 / 6 3,115× 1.84e-11 6.59e-9 ✓ sig.
detection of visible light
OPN1SW, OPN1LW, OPN1MW
 GO:0009584 3 / 15 1,246× 4.18e-10 1.10e-7 ✓ sig.
cellular response to light stimulus
OPN1SW, OPN1LW, OPN1MW
 GO:0071482 3 / 16 1,168× 5.15e-10 1.32e-7 ✓ sig.
phototransduction
OPN1SW, OPN1LW, OPN1MW
 GO:0007602 3 / 34 550× 5.50e-9 1.05e-6 ✓ sig.
visual perception
OPN1SW, OPN1LW, OPN1MW
 GO:0007601 3 / 215 86.9× 1.50e-6 1.20e-4 ✓ sig.
positive regulation of cytokinesis
OPN1LW, OPN1MW
 GO:0032467 2 / 41 304× 1.41e-5 7.09e-4 ✓ sig.
G protein-coupled receptor signaling pathway
OPN1SW, OPN1LW, OPN1MW
 GO:0007186 3 / 1,031 18.1× 1.67e-4 4.47e-3 ✓ sig.
signal transduction
OPN1SW, OPN1LW, OPN1MW
 GO:0007165 3 / 2,125 8.8× 1.47e-3 1.81e-2 ✓ sig.
cellular response to UV-A
OPN1SW
 GO:0071492 1 / 11 566× 1.76e-3 1.99e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cone monochromatism X-linked cone dysfunction syndrome with myopia 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Blue cone monochromatism Cone monochromatism 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Blue cone monochromatism X-linked cone dysfunction syndrome with myopia 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Colorblindness, partial, protan series Red color blindness 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorblindness, partial, protan series Cone monochromatism 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colorblindness, partial, protan series X-linked cone dysfunction syndrome with myopia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cone monochromatism Red color blindness 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Red color blindness X-linked cone dysfunction syndrome with myopia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Blue cone monochromatism Tritan color blindness 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blue cone monochromatism Red color blindness 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blue cone monochromatism Colorblindness, partial, protan series 0.250 1 1.94e-4 4.41e-4 ✓ sig.