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 118

10 diseases · 21 shared-gene connections
10 Diseases
32 Unique genes
0.197 Avg. similarity score
Metachromatic leukodystrophy Most-connected disease (8 links)
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Disease Searched: Gaucher disease due to saposin C deficiency 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 ⇵
Metachromatic leukodystrophy 8 8 8
Combined saposin deficiency 6 6 2
Retinitis pigmentosa-deafness syndrome 6 6 11
Combined psap deficiency 5 5 1
Gaucher disease due to saposin C deficiency 5 5 1
Krabbe disease due to saposin A deficiency 5 5 1
Gaucher disease 4 4 17
Alexander disease 1 1 1
Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome 1 1 1
mucopolysaccharidosis type 6 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PSAP 7 / 10 Combined psap deficiency, Combined saposin deficiency, Gaucher disease, Gaucher disease due to saposin C deficiency and 3 more
CDH23 4 / 10 Combined saposin deficiency, Gaucher disease, Metachromatic leukodystrophy, Retinitis pigmentosa-deafness syndrome
ARSB 2 / 10 Metachromatic leukodystrophy, mucopolysaccharidosis type 6
GBA1 2 / 10 Gaucher disease, Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome
GFAP 2 / 10 Alexander disease, Metachromatic leukodystrophy
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 ⇵
Glycosphingolipid metabolism
PSAP, SMPD1, ARSA, ARSB
 Reactome 4 / 46 32.6× 6.26e-6 2.42e-4 ✓ sig.
Lysosome
PSAP, SMPD1, SCARB2, ARSA, ARSB
 KEGG 5 / 133 14.1× 2.45e-5 7.47e-4 ✓ sig.
Sphingolipid metabolism
PSAP, SMPD1, ARSA
 KEGG 3 / 54 20.9× 3.89e-4 6.79e-3 ✓ sig.
The activation of arylsulfatases
ARSA, ARSB
 Reactome 2 / 13 57.7× 5.27e-4 8.61e-3 ✓ sig.
Cytosolic tRNA aminoacylation
YARS1, HARS1
 Reactome 2 / 24 31.3× 1.83e-3 2.22e-2 ✓ sig.
MPS VI - Maroteaux-Lamy syndrome
ARSB
 Reactome 1 / 1 375× 2.66e-3 2.91e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH6
MSH6
 Reactome 1 / 2 188× 5.32e-3 4.72e-2 ✓ sig.
NTF3 activates NTRK3 signaling
NTRK3
 Reactome 1 / 2 188× 5.32e-3 4.72e-2 ✓ sig.
Type II diabetes mellitus
PKLR, TNF
 KEGG 2 / 47 16.0× 6.90e-3 5.60e-2
Defective Mismatch Repair Associated With MSH2
MSH6
 Reactome 1 / 3 125× 7.97e-3 6.13e-2
Activated NTRK3 signals through PLCG1
NTRK3
 Reactome 1 / 3 125× 7.97e-3 6.13e-2
Activated NTRK3 signals through PI3K
NTRK3
 Reactome 1 / 3 125× 7.97e-3 6.13e-2
Aminoacyl-tRNA biosynthesis
YARS1, HARS1
 KEGG 2 / 66 11.4× 1.33e-2 8.41e-2
Renin secretion
ACE, ADRB1
 KEGG 2 / 69 10.9× 1.44e-2 8.85e-2
TNFR1-mediated ceramide production
TNF
 Reactome 1 / 6 62.6× 1.59e-2 9.38e-2

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
sensory perception of light stimulus
CDH23, CLRN1, MYO7A, PCDH15, USH1G, USH2A, WHRN
 GO:0050953 7 / 13 314× 3.64e-17 3.67e-14 ✓ sig.
equilibrioception
CDH23, CLRN1, MYO7A, PCDH15, USH1G
 GO:0050957 5 / 6 487× 6.36e-14 3.61e-11 ✓ sig.
photoreceptor cell maintenance
CDH23, CLN8, CLRN1, CRB1, PCDH15, USH1G, USH2A
 GO:0045494 7 / 45 90.8× 9.26e-13 4.31e-10 ✓ sig.
sensory perception of sound
CDH23, SCARB2, CLRN1, MYO7A, PCDH15, USH1G, USH2A, WHRN
 GO:0007605 8 / 162 28.8× 2.36e-10 6.28e-8 ✓ sig.
inner ear receptor cell differentiation
MYO7A, USH1G, USH2A, WHRN
 GO:0060113 4 / 9 260× 8.87e-10 2.03e-7 ✓ sig.
auditory receptor cell stereocilium organization
CDH23, CLRN1, MYO7A, WHRN
 GO:0060088 4 / 19 123× 2.70e-8 4.04e-6 ✓ sig.
inner ear receptor cell stereocilium organization
CDH23, MYO7A, USH1G, WHRN
 GO:0060122 4 / 25 93.4× 8.73e-8 1.09e-5 ✓ sig.
visual perception
CDH23, CLN8, CLRN1, CRB1, MYO7A, USH2A
 GO:0007601 6 / 215 16.3× 1.53e-6 1.20e-4 ✓ sig.
inner ear auditory receptor cell differentiation
CDH23, MYO7A, USH2A
 GO:0042491 3 / 19 92.2× 4.34e-6 2.76e-4 ✓ sig.
mechanoreceptor differentiation
NTRK3, MYO7A
 GO:0042490 2 / 5 234× 2.83e-5 1.21e-3 ✓ sig.
cochlea development
CDH23, NTRK3, MYO7A
 GO:0090102 3 / 35 50.1× 2.88e-5 1.22e-3 ✓ sig.
mitochondrial membrane organization
CLN8, SNCA
 GO:0007006 2 / 7 167× 5.93e-5 2.11e-3 ✓ sig.
inner ear development
CDH23, MYO7A, PCDH15
 GO:0048839 3 / 54 32.4× 1.07e-4 3.28e-3 ✓ sig.
neuronal action potential propagation
NTRK3, CLCN1
 GO:0019227 2 / 11 106× 1.55e-4 4.32e-3 ✓ sig.
lysosome organization
CLN8, ARSB, MYO7A
 GO:0007040 3 / 65 27.0× 1.85e-4 4.95e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Combined saposin deficiency Metachromatic leukodystrophy 0.222 2 2.36e-7 1.55e-6 ✓ sig.
Combined saposin deficiency Retinitis pigmentosa-deafness syndrome 0.167 2 4.64e-7 2.90e-6 ✓ sig.
Combined saposin deficiency Gaucher disease 0.111 2 1.15e-6 6.66e-6 ✓ sig.
Metachromatic leukodystrophy Retinitis pigmentosa-deafness syndrome 0.111 2 1.30e-5 6.32e-5 ✓ sig.
Gaucher disease Metachromatic leukodystrophy 0.083 2 3.20e-5 1.48e-4 ✓ sig.
Gaucher disease due to saposin C deficiency Krabbe disease due to saposin A deficiency 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Combined psap deficiency Krabbe disease due to saposin A deficiency 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Combined psap deficiency Gaucher disease due to saposin C deficiency 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Gaucher disease Retinitis pigmentosa-deafness syndrome 0.074 2 6.27e-5 2.33e-4 ✓ sig.
Combined saposin deficiency Gaucher disease due to saposin C deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Combined saposin deficiency Krabbe disease due to saposin A deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Combined psap deficiency Combined saposin deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Combined psap deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Alexander disease Metachromatic leukodystrophy 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Gaucher disease due to saposin C deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Krabbe disease due to saposin A deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Metachromatic leukodystrophy mucopolysaccharidosis type 6 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Combined psap deficiency Retinitis pigmentosa-deafness syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Gaucher disease due to saposin C deficiency Retinitis pigmentosa-deafness syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Krabbe disease due to saposin A deficiency Retinitis pigmentosa-deafness syndrome 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Gaucher disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome 0.056 1 1.10e-3 1.83e-3 ✓ sig.