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.

← Back to all clusters

Cluster 432

5 diseases · 7 shared-gene connections
5 Diseases
2 Unique genes
0.405 Avg. similarity score
X-linked ocular abinism Most-connected disease (4 links)
Log in to save this analysis

Save This Analysis

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 ⇵
X-linked ocular abinism 4 4 2
Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency 3 3 1
Ocular albinism with sensorineural deafness 3 3 1
hermansky-pudlak syndrome 10 3 3 1
GPR143-related foveal hypoplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AP3D1 4 / 5 Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency, hermansky-pudlak syndrome 10, Ocular albinism with sensorineural deafness, X-linked ocular abinism
GPR143 2 / 5 GPR143-related foveal hypoplasia, X-linked ocular abinism
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 ⇵
Amine ligand-binding receptors
GPR143
 Reactome 1 / 7 858× 1.17e-3 1.52e-2 ✓ sig.
Lysosome
AP3D1
 KEGG 1 / 133 45.2× 2.20e-2 1.09e-1
G alpha (q) signalling events
GPR143
 Reactome 1 / 172 34.9× 2.84e-2 1.25e-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 ⇵
melanosome organization
AP3D1, GPR143
 GO:0032438 2 / 25 747× 1.72e-6 1.28e-4 ✓ sig.
regulation of melanosome transport
GPR143
 GO:1902908 1 / 1 9,344× 1.07e-4 3.18e-3 ✓ sig.
neurotransmitter receptor transport, postsynaptic endosome to lysosome
AP3D1
 GO:0098943 1 / 2 4,672× 2.14e-4 5.28e-3 ✓ sig.
eye pigment biosynthetic process
GPR143
 GO:0006726 1 / 2 4,672× 2.14e-4 5.28e-3 ✓ sig.
regulation of melanosome organization
GPR143
 GO:1903056 1 / 2 4,672× 2.14e-4 5.28e-3 ✓ sig.
synaptic vesicle budding from endosome
AP3D1
 GO:0016182 1 / 3 3,115× 3.21e-4 7.03e-3 ✓ sig.
zinc ion import into lysosome
AP3D1
 GO:0140916 1 / 4 2,336× 4.28e-4 8.59e-3 ✓ sig.
positive regulation of NK T cell differentiation
AP3D1
 GO:0051138 1 / 4 2,336× 4.28e-4 8.59e-3 ✓ sig.
synaptic vesicle coating
AP3D1
 GO:0016183 1 / 5 1,869× 5.35e-4 9.98e-3 ✓ sig.
synaptic vesicle membrane organization
AP3D1
 GO:0048499 1 / 5 1,869× 5.35e-4 9.98e-3 ✓ sig.
melanosome localization
GPR143
 GO:0032400 1 / 5 1,869× 5.35e-4 9.98e-3 ✓ sig.
clathrin-coated vesicle cargo loading, AP-3-mediated
AP3D1
 GO:0035654 1 / 7 1,335× 7.49e-4 1.25e-2 ✓ sig.
antigen processing and presentation, exogenous lipid antigen via MHC class Ib
AP3D1
 GO:0048007 1 / 7 1,335× 7.49e-4 1.25e-2 ✓ sig.
Golgi to vacuole transport
AP3D1
 GO:0006896 1 / 9 1,038× 9.63e-4 1.47e-2 ✓ sig.
endosome to melanosome transport
AP3D1
 GO:0035646 1 / 10 934× 1.07e-3 1.57e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency Ocular albinism with sensorineural deafness 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency hermansky-pudlak syndrome 10 0.500 1 6.49e-5 2.34e-4 ✓ sig.
hermansky-pudlak syndrome 10 Ocular albinism with sensorineural deafness 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Early-onset severe hermansky-pudlak syndrome with hearing loss due to ap3d1 deficiency X-linked ocular abinism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
GPR143-related foveal hypoplasia X-linked ocular abinism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
hermansky-pudlak syndrome 10 X-linked ocular abinism 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ocular albinism with sensorineural deafness X-linked ocular abinism 0.333 1 1.30e-4 3.90e-4 ✓ sig.