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 114

11 diseases · 22 shared-gene connections
11 Diseases
48 Unique genes
0.253 Avg. similarity score
Metachromatic leukodystrophy 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 ⇵
Metachromatic leukodystrophy 8 8 8
Combined saposin deficiency 6 6 2
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
metachromatic leukodystrophy due to saposin B deficiency 5 5 1
Gaucher disease 4 4 17
Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome 2 2 1
Hereditary parkinson disease 2 2 28
Alexander disease 1 1 1
mucopolysaccharidosis type 6 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PSAP 8 / 11 Combined psap deficiency, Combined saposin deficiency, Gaucher disease, Gaucher disease due to saposin C deficiency and 4 more
CDH23 3 / 11 Combined saposin deficiency, Gaucher disease, Metachromatic leukodystrophy
GBA1 3 / 11 Gaucher disease, Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome, Hereditary parkinson disease
ARSB 2 / 11 Metachromatic leukodystrophy, mucopolysaccharidosis type 6
GFAP 2 / 11 Alexander disease, Metachromatic leukodystrophy
SNCA 2 / 11 Gaucher disease, Hereditary parkinson disease
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 ⇵
Pathways of neurodegeneration - multiple diseases
SNCA, TNF, LRRK2, MAPT, ATXN2, ATXN3, ND1, PARK7, PINK1, PRKN, SNCAIP
 KEGG 11 / 480 5.7× 2.19e-6 9.50e-5 ✓ sig.
Parkinson disease
SNCA, LRRK2, MAPT, ND1, PARK7, PINK1, PRKN, SNCAIP
 KEGG 8 / 268 7.5× 9.64e-6 3.26e-4 ✓ sig.
Glycosphingolipid metabolism
PSAP, SMPD1, ARSA, ARSB
 Reactome 4 / 46 21.8× 3.24e-5 8.90e-4 ✓ sig.
Lysosome
PSAP, SMPD1, SCARB2, ARSA, ARSB
 KEGG 5 / 133 9.4× 1.80e-4 3.61e-3 ✓ sig.
Josephin domain DUBs
ATXN3, PRKN
 Reactome 2 / 12 41.7× 1.01e-3 1.36e-2 ✓ sig.
The activation of arylsulfatases
ARSA, ARSB
 Reactome 2 / 13 38.5× 1.19e-3 1.54e-2 ✓ sig.
Sphingolipid metabolism
PSAP, SMPD1, ARSA
 KEGG 3 / 54 13.9× 1.29e-3 1.64e-2 ✓ sig.
Pink/Parkin Mediated Mitophagy
PINK1, PRKN
 Reactome 2 / 22 22.7× 3.43e-3 3.39e-2 ✓ sig.
Mismatch repair
MSH6, RFC1
 KEGG 2 / 23 21.8× 3.75e-3 3.60e-2 ✓ sig.
MPS VI - Maroteaux-Lamy syndrome
ARSB
 Reactome 1 / 1 250× 4.00e-3 3.77e-2 ✓ sig.
Asthma
TNF, HLA-DRA
 KEGG 2 / 32 15.6× 7.19e-3 5.56e-2
Defective Mismatch Repair Associated With MSH6
MSH6
 Reactome 1 / 2 125× 7.98e-3 5.96e-2
NTF3 activates NTRK3 signaling
NTRK3
 Reactome 1 / 2 125× 7.98e-3 5.96e-2
Amyloid fiber formation
SNCA, PRKN, SNCAIP
 Reactome 3 / 109 6.9× 9.35e-3 6.59e-2
Allograft rejection
TNF, HLA-DRA
 KEGG 2 / 39 12.8× 1.05e-2 7.10e-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 ⇵
adult locomotory behavior
CLN8, SNCA, GIGYF2, NR4A2, PARK7, PRKN
 GO:0008344 6 / 56 41.7× 6.12e-9 1.12e-6 ✓ sig.
regulation of reactive oxygen species metabolic process
SNCA, TNF, LRRK2, PINK1, PRKN
 GO:2000377 5 / 27 72.1× 6.98e-9 1.25e-6 ✓ sig.
regulation of synaptic vesicle transport
LRRK2, PINK1, PRKN
 GO:1902803 3 / 3 389× 1.59e-8 2.56e-6 ✓ sig.
mitochondrion to lysosome vesicle-mediated transport
VPS35, PINK1, PRKN
 GO:0099074 3 / 3 389× 1.59e-8 2.56e-6 ✓ sig.
dopamine metabolic process
SNCA, NR4A2, PRKN, SNCAIP
 GO:0042417 4 / 18 86.5× 1.14e-7 1.35e-5 ✓ sig.
negative regulation of mitochondrial fission
MAPT, PINK1, PRKN
 GO:0090258 3 / 5 234× 1.58e-7 1.78e-5 ✓ sig.
positive regulation of protein localization to cell periphery
SNCA, VPS35, EIF4G1
 GO:1904377 3 / 5 234× 1.58e-7 1.78e-5 ✓ sig.
negative regulation of neuron apoptotic process
CLN8, SNCA, FGF20, NR4A2, PARK7, PINK1, PRKN
 GO:0043524 7 / 160 17.0× 1.62e-7 1.82e-5 ✓ sig.
dopamine uptake involved in synaptic transmission
SNCA, PARK7, PRKN
 GO:0051583 3 / 6 195× 3.16e-7 3.18e-5 ✓ sig.
cellular response to oxidative stress
SNCA, LRRK2, NR4A2, PARK7, PINK1, PRKN
 GO:0034599 6 / 111 21.0× 3.84e-7 3.74e-5 ✓ sig.
regulation of presynapse assembly
NTRK3, SNCA, VPS35, EIF4G1
 GO:1905606 4 / 29 53.7× 8.68e-7 7.39e-5 ✓ sig.
cellular response to toxic substance
TNF, PINK1, PRKN
 GO:0097237 3 / 12 97.3× 3.44e-6 2.23e-4 ✓ sig.
negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
PARK7, PINK1, PRKN
 GO:1903377 3 / 14 83.4× 5.68e-6 3.32e-4 ✓ sig.
negative regulation of late endosome to lysosome transport
LRRK2, VPS35
 GO:1902823 2 / 2 389× 6.46e-6 3.68e-4 ✓ sig.
positive regulation of dopamine biosynthetic process
VPS35, PARK7
 GO:1903181 2 / 2 389× 6.46e-6 3.68e-4 ✓ 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 1.64e-6 ✓ sig.
Combined saposin deficiency Gaucher disease 0.111 2 1.15e-6 7.04e-6 ✓ sig.
Gaucher disease Hereditary parkinson disease 0.070 3 3.60e-6 2.03e-5 ✓ sig.
Gaucher disease Metachromatic leukodystrophy 0.083 2 3.20e-5 1.56e-4 ✓ sig.
Combined psap deficiency metachromatic leukodystrophy due to saposin B deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Krabbe disease due to saposin A deficiency metachromatic leukodystrophy due to saposin B deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Gaucher disease due to saposin C deficiency Krabbe disease due to saposin A deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Gaucher disease due to saposin C deficiency metachromatic leukodystrophy due to saposin B deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Combined psap deficiency Krabbe disease due to saposin A deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Combined psap deficiency Gaucher disease due to saposin C deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Combined saposin deficiency Krabbe disease due to saposin A deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined saposin deficiency Gaucher disease due to saposin C deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined saposin deficiency metachromatic leukodystrophy due to saposin B deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined psap deficiency Combined saposin deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined psap deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Gaucher disease due to saposin C deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Krabbe disease due to saposin A deficiency Metachromatic leukodystrophy 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Alexander disease Metachromatic leukodystrophy 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Metachromatic leukodystrophy metachromatic leukodystrophy due to saposin B deficiency 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Metachromatic leukodystrophy mucopolysaccharidosis type 6 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Gaucher disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Hereditary parkinson disease 0.034 1 1.82e-3 2.66e-3 ✓ sig.