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 191

8 diseases · 12 shared-gene connections
8 Diseases
54 Unique genes
0.186 Avg. similarity score
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome Most-connected disease (4 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 ⇵
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome 4 4 1
Distal anoctaminopathy 4 4 1
Rhabdomyolysis 4 4 8
Visual disorder 4 4 20
gnathodiaphyseal dysplasia 4 4 1
Neuronal ceroid lipofuscinosis 2 2 31
Acrokeratosis verruciformis 1 1 1
adult neuronal ceroid lipofuscinosis 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
ANO5 5 / 8 Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome, Distal anoctaminopathy, gnathodiaphyseal dysplasia, Rhabdomyolysis and 1 more
ATP2A2 2 / 8 Acrokeratosis verruciformis, Rhabdomyolysis
CLN3 2 / 8 Neuronal ceroid lipofuscinosis, Visual disorder
CLN5 2 / 8 Neuronal ceroid lipofuscinosis, Visual disorder
CLN6 2 / 8 Neuronal ceroid lipofuscinosis, Visual disorder
CTSF 2 / 8 adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis
DNAJC5 2 / 8 adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis
PPT1 2 / 8 Neuronal ceroid lipofuscinosis, Visual disorder
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 ⇵
Lysosome
CTSF, PPT1, CLN5, CTSD, TPP1, CLN3, SMPD1, MFSD8
 KEGG 8 / 133 13.4× 1.24e-7 7.89e-6 ✓ sig.
Signal attenuation
MAPK1, MAPK3, INS
 Reactome 3 / 10 66.7× 1.01e-5 3.38e-4 ✓ sig.
Insulin signaling pathway
PPARGC1A, RPS6KB1, GSK3B, MAPK1, MAPK3, INS
 KEGG 6 / 138 9.7× 3.39e-5 9.26e-4 ✓ sig.
Apelin signaling pathway
PPARGC1A, RPS6KB1, TFAM, MAPK1, MAPK3, RYR2
 KEGG 6 / 140 9.5× 3.67e-5 9.89e-4 ✓ sig.
Longevity regulating pathway
PPARGC1A, RPS6KB1, SIRT1, SOD2, INS
 KEGG 5 / 90 12.4× 5.00e-5 1.28e-3 ✓ sig.
Transcriptional activation of mitochondrial biogenesis
PPARGC1A, TFAM, SOD2, NCOR1
 Reactome 4 / 51 17.4× 7.80e-5 1.83e-3 ✓ sig.
Longevity regulating pathway - multiple species
RPS6KB1, SIRT1, SOD2, INS
 KEGG 4 / 62 14.3× 1.68e-4 3.41e-3 ✓ sig.
Thyroid hormone signaling pathway
ATP2A2, GSK3B, MAPK1, MAPK3, NCOR1
 KEGG 5 / 122 9.1× 2.12e-4 4.08e-3 ✓ sig.
Regulation of HSF1-mediated heat shock response
SIRT1, GSK3B, MAPK1, MAPK3
 Reactome 4 / 69 12.9× 2.54e-4 4.70e-3 ✓ sig.
Prolactin signaling pathway
GSK3B, MAPK1, MAPK3, INS
 KEGG 4 / 71 12.5× 2.84e-4 5.14e-3 ✓ sig.
Negative feedback regulation of MAPK pathway
MAPK1, MAPK3
 Reactome 2 / 6 74.1× 2.94e-4 5.28e-3 ✓ sig.
Diabetic cardiomyopathy
ATP2A2, PARP1, CTSD, GSK3B, INS, RYR2
 KEGG 6 / 205 6.5× 3.00e-4 5.36e-3 ✓ sig.
FoxO signaling pathway
SIRT1, MAPK1, MAPK3, SOD2, INS
 KEGG 5 / 133 8.4× 3.16e-4 5.59e-3 ✓ sig.
Apoptosis
CTSF, PARP1, CTSD, MAPK1, MAPK3
 KEGG 5 / 137 8.1× 3.62e-4 6.21e-3 ✓ sig.
Suppression of apoptosis
MAPK1, MAPK3
 Reactome 2 / 7 63.5× 4.11e-4 6.85e-3 ✓ 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 ⇵
lysosome organization
PPT1, CLN5, CLN8, GRN, TPP1, CLN3, CLN6, MFSD8
 GO:0007040 8 / 65 42.6× 1.26e-11 4.54e-9 ✓ sig.
negative regulation of neuron apoptotic process
DNAJC5, PPARGC1A, PPT1, SIRT1, CLN8, GRN, CLN3, MFSD8, SOD2
 GO:0043524 9 / 160 19.5× 7.55e-10 1.74e-7 ✓ sig.
lysosomal lumen acidification
PPT1, CLN5, GRN, CLN3, CLN6
 GO:0007042 5 / 25 69.2× 8.47e-9 1.49e-6 ✓ sig.
tRNA-type intron splice site recognition and cleavage
TSEN2, TSEN34, TSEN54
 GO:0000379 3 / 3 346× 2.28e-8 3.49e-6 ✓ sig.
macromolecule catabolic process
PPT1, CLN8, CLN6
 GO:0009057 3 / 3 346× 2.28e-8 3.49e-6 ✓ sig.
mitochondrion organization
FIS1, MFN1, PARP1, PPARGC1A, GSK3B, MFSD8, SOD2
 GO:0007005 7 / 130 18.6× 9.04e-8 1.11e-5 ✓ sig.
lysosomal protein catabolic process
GRN, TPP1, CLN3, MFSD8
 GO:1905146 4 / 16 86.5× 1.10e-7 1.31e-5 ✓ sig.
insulin receptor signaling pathway
RPS6KB1, GSK3B, MAPK1, MAPK3, INS
 GO:0008286 5 / 80 21.6× 3.40e-6 2.21e-4 ✓ sig.
Bergmann glial cell differentiation
GFAP, MAPK1, MAPK3
 GO:0060020 3 / 11 94.4× 3.70e-6 2.36e-4 ✓ sig.
tRNA splicing, via endonucleolytic cleavage and ligation
TSEN2, TSEN34, TSEN54
 GO:0006388 3 / 13 79.9× 6.39e-6 3.65e-4 ✓ sig.
protein catabolic process
PPT1, CLN5, CLN8, TPP1, CLN6
 GO:0030163 5 / 97 17.8× 8.78e-6 4.72e-4 ✓ sig.
cellular response to oxygen-containing compound
PARP1, GSK3B, INS
 GO:1901701 3 / 16 64.9× 1.24e-5 6.19e-4 ✓ sig.
neuromuscular process controlling balance
CLN8, TPP1, CLN3, MYH10
 GO:0050885 4 / 53 26.1× 1.64e-5 7.70e-4 ✓ sig.
cellular response to oxidative stress
ATP2A2, PARP1, PPARGC1A, ATP13A2, SOD2
 GO:0034599 5 / 111 15.6× 1.69e-5 7.89e-4 ✓ sig.
negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
SIRT1, SOD2, INS
 GO:1902176 3 / 18 57.7× 1.80e-5 8.28e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Neuronal ceroid lipofuscinosis Visual disorder 0.083 4 6.37e-8 4.88e-7 ✓ sig.
adult neuronal ceroid lipofuscinosis Neuronal ceroid lipofuscinosis 0.063 2 3.92e-6 2.19e-5 ✓ sig.
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome Distal anoctaminopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome gnathodiaphyseal dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Distal anoctaminopathy gnathodiaphyseal dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Acrokeratosis verruciformis Rhabdomyolysis 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome Rhabdomyolysis 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Distal anoctaminopathy Rhabdomyolysis 0.111 1 5.20e-4 1.04e-3 ✓ sig.
gnathodiaphyseal dysplasia Rhabdomyolysis 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Asymptomatic hyperckemia-myalgia-rhabdomyolysis syndrome Visual disorder 0.048 1 1.30e-3 2.04e-3 ✓ sig.
Distal anoctaminopathy Visual disorder 0.048 1 1.30e-3 2.04e-3 ✓ sig.
gnathodiaphyseal dysplasia Visual disorder 0.048 1 1.30e-3 2.04e-3 ✓ sig.