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 178

9 diseases · 8 shared-gene connections
9 Diseases
11 Unique genes
0.083 Avg. similarity score
Hermansky-pudlak syndrome Most-connected disease (8 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 ⇵
Hermansky-pudlak syndrome 8 8 11
hermansky-pudlak syndrome 1 1 1 1
hermansky-pudlak syndrome 11 1 1 1
hermansky-pudlak syndrome 2 1 1 1
hermansky-pudlak syndrome 4 1 1 1
hermansky-pudlak syndrome 5 1 1 1
hermansky-pudlak syndrome 6 1 1 1
hermansky-pudlak syndrome 8 1 1 1
hermansky-pudlak syndrome 9 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AP3B1 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 2
BLOC1S3 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 8
BLOC1S5 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 11
BLOC1S6 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 9
HPS1 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 1
HPS4 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 4
HPS5 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 5
HPS6 2 / 9 Hermansky-pudlak syndrome, hermansky-pudlak syndrome 6
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 ⇵
Golgi Associated Vesicle Biogenesis
AP3B1, BLOC1S3, BLOC1S6, DTNBP1
 Reactome 4 / 56 78.0× 1.37e-7 8.57e-6 ✓ sig.
RAB GEFs exchange GTP for GDP on RABs
HPS1, HPS4
 Reactome 2 / 90 24.3× 2.92e-3 3.02e-2 ✓ sig.
Lysosome
AP3B1, AP3D1
 KEGG 2 / 133 16.4× 6.27e-3 5.08e-2
Signaling by BRAF and RAF fusions
AP3B1
 Reactome 1 / 67 16.3× 5.97e-2 1.88e-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 ⇵
platelet dense granule organization
AP3B1, AP3D1, BLOC1S3, DTNBP1, HPS1, HPS3, HPS4, HPS5, HPS6
 GO:0060155 9 / 25 612× 1.47e-25 4.94e-22 ✓ sig.
melanosome assembly
AP3B1, AP3D1, HPS1, HPS3, HPS4, HPS5, HPS6
 GO:1903232 7 / 19 626× 1.05e-19 1.64e-16 ✓ sig.
anterograde synaptic vesicle transport
AP3B1, AP3D1, BLOC1S3, BLOC1S5, BLOC1S6, DTNBP1
 GO:0048490 6 / 17 600× 9.65e-17 9.35e-14 ✓ sig.
melanosome organization
AP3B1, AP3D1, BLOC1S3, BLOC1S5, BLOC1S6, DTNBP1
 GO:0032438 6 / 25 408× 1.38e-15 1.04e-12 ✓ sig.
anterograde axonal transport
AP3B1, AP3D1, BLOC1S3, BLOC1S5, BLOC1S6, DTNBP1
 GO:0008089 6 / 29 351× 3.69e-15 2.63e-12 ✓ sig.
pigmentation
AP3B1, BLOC1S3, BLOC1S6, HPS3, HPS5, HPS6
 GO:0043473 6 / 39 261× 2.53e-14 1.53e-11 ✓ sig.
blood coagulation
AP3B1, BLOC1S3, BLOC1S6, DTNBP1, HPS4, HPS5, HPS6
 GO:0007596 7 / 106 112× 5.01e-14 2.89e-11 ✓ sig.
endosome to melanosome transport
AP3D1, BLOC1S3, BLOC1S5, BLOC1S6
 GO:0035646 4 / 10 680× 1.36e-11 4.86e-9 ✓ sig.
protein targeting
AP3B1, AP3D1, BLOC1S6, HPS4
 GO:0006605 4 / 49 139× 1.36e-8 2.23e-6 ✓ sig.
developmental pigmentation
BLOC1S3, BLOC1S5, HPS5
 GO:0048066 3 / 14 364× 5.50e-8 7.35e-6 ✓ sig.
protein transmembrane transport
BLOC1S3, BLOC1S6, DTNBP1
 GO:0071806 3 / 19 268× 1.46e-7 1.67e-5 ✓ sig.
melanosome transport
BLOC1S3, BLOC1S5, BLOC1S6
 GO:0032402 3 / 22 232× 2.32e-7 2.45e-5 ✓ sig.
positive regulation of pigment cell differentiation
BLOC1S5, BLOC1S6
 GO:0050942 2 / 2 1,699× 3.15e-7 3.17e-5 ✓ sig.
vesicle-mediated transport
AP3B1, AP3D1, BLOC1S5, HPS1, HPS4
 GO:0016192 5 / 326 26.1× 6.64e-7 5.94e-5 ✓ sig.
neuron projection development
BLOC1S3, BLOC1S5, BLOC1S6, DTNBP1
 GO:0031175 4 / 161 42.2× 1.67e-6 1.25e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hermansky-pudlak syndrome hermansky-pudlak syndrome 8 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 2 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 1 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 11 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 4 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 5 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 6 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Hermansky-pudlak syndrome hermansky-pudlak syndrome 9 0.083 1 7.14e-4 1.31e-3 ✓ sig.