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 92

12 diseases · 16 shared-gene connections
12 Diseases
227 Unique genes
0.033 Avg. similarity score
Spinocerebellar ataxia Most-connected disease (9 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 ⇵
Spinocerebellar ataxia 9 9 104
Cerebellar ataxia 6 6 114
Spastic ataxia 4 4 70
spinocerebellar ataxia type 42 3 3 1
autosomal recessive cerebellar ataxia 2 2 1
spinocerebellar ataxia, autosomal recessive 23 2 2 1
3m syndrome 1 1 3
Cayman type cerebellar ataxia 1 1 1
Spastic ataxia optic atrophy dysarthria syndrome 1 1 1
spinocerebellar ataxia type 13 1 1 1
spinocerebellar ataxia, autosomal recessive 27 1 1 1
spinocerebellar ataxia, autosomal recessive 28 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CACNA1G 4 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia, spinocerebellar ataxia type 42
AFG3L2 3 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia
CACNA1A 3 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia
CWF19L1 3 / 12 autosomal recessive cerebellar ataxia, Cerebellar ataxia, Spinocerebellar ataxia
ITPR1 3 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia
SETX 3 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia
SYNE1 3 / 12 Cerebellar ataxia, Spastic ataxia, Spinocerebellar ataxia
TDP2 3 / 12 Cerebellar ataxia, Spinocerebellar ataxia, spinocerebellar ataxia, autosomal recessive 23
ANO10 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
ATCAY 2 / 12 Cayman type cerebellar ataxia, Cerebellar ataxia
CA8 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
CCDC8 2 / 12 3m syndrome, Spinocerebellar ataxia
CCDC88C 2 / 12 Spastic ataxia, Spinocerebellar ataxia
COQ4 2 / 12 Cerebellar ataxia, Spastic ataxia
COQ8A 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
COX3 2 / 12 Cerebellar ataxia, Spastic ataxia
DAB1 2 / 12 Spastic ataxia, Spinocerebellar ataxia
DNMT1 2 / 12 Cerebellar ataxia, Spastic ataxia
ELOVL4 2 / 12 Spastic ataxia, Spinocerebellar ataxia
ERCC4 2 / 12 Cerebellar ataxia, Spastic ataxia
ESR1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
FAT2 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
FGF14 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
FLNC 2 / 12 Cerebellar ataxia, Spastic ataxia
GDAP2 2 / 12 Spinocerebellar ataxia, spinocerebellar ataxia, autosomal recessive 27
GRM1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
HARS1 2 / 12 Cerebellar ataxia, Spastic ataxia
JMJD8 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
KCNC3 2 / 12 Spinocerebellar ataxia, spinocerebellar ataxia type 13
KIF1C 2 / 12 Cerebellar ataxia, Spastic ataxia
MTPAP 2 / 12 Spastic ataxia, Spastic ataxia optic atrophy dysarthria syndrome
NOP56 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
NPTX1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PDYN 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PEX6 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PIK3R5 2 / 12 Spastic ataxia, Spinocerebellar ataxia
PITRM1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PLA2G6 2 / 12 Cerebellar ataxia, Spastic ataxia
PMPCA 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PNPLA6 2 / 12 Cerebellar ataxia, Spastic ataxia
POLG 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
POLR3A 2 / 12 Cerebellar ataxia, Spastic ataxia
PRDX3 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PRKCG 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
PUM1 2 / 12 Spastic ataxia, Spinocerebellar ataxia
RHBDL1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
RUBCN 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
SCN8A 2 / 12 Cerebellar ataxia, Spastic ataxia
SEPSECS 2 / 12 Cerebellar ataxia, Spastic ataxia
SLC36A1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
SNX14 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
SPTBN2 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
STUB1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
STXBP1 2 / 12 Cerebellar ataxia, Spastic ataxia
SYT14 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
TDP1 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
THG1L 2 / 12 Spinocerebellar ataxia, spinocerebellar ataxia, autosomal recessive 28
TTBK2 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
TUBB6 2 / 12 Spastic ataxia, Spinocerebellar ataxia
VPS13D 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
VPS41 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
WDR24 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
WWOX 2 / 12 Cerebellar ataxia, Spinocerebellar ataxia
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 ⇵
Spinocerebellar ataxia
AFG3L2, ATXN1, ATXN1L, ATXN2, CACNA1A, FGF14, GRM1, NOP56, PRKCG, SPTBN2, TRPC3, ITPR1
 KEGG 23 / 144 8.5× 2.66e-15 9.40e-13 ✓ sig.
Pathways of neurodegeneration - multiple diseases
ATXN1, ATXN1L, ATXN2, GRM1, LRRK2, PRKCG, SPTBN2, TRPC3, ITPR1, PDYN, COX3, ATP6
 KEGG 30 / 480 3.3× 7.45e-9 6.77e-7 ✓ sig.
Parkinson disease
LRRK2, ITPR1, COX3, ATP6, ATP8, COX1, COX2, MFN2, ND1, ND2, ND3, ND4
 KEGG 19 / 268 3.8× 7.67e-7 3.87e-5 ✓ sig.
Oxidative phosphorylation
COX3, ATP6, ATP6V0A1, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 13 / 137 5.0× 1.88e-6 8.34e-5 ✓ sig.
Prion disease
ITPR1, COX3, ATP6, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 18 / 275 3.5× 4.70e-6 1.81e-4 ✓ sig.
Huntington disease
EP300, ITPR1, COX3, ATP6, ATP8, COX1, COX2, KCNJ10, ND1, ND2, ND3, ND4
 KEGG 19 / 308 3.3× 6.02e-6 2.20e-4 ✓ sig.
Respiratory electron transport
COX3, COX1, COX2, ND1, ND2, ND3, ND4, ND5, SURF1
 Reactome 9 / 83 5.7× 2.56e-5 7.30e-4 ✓ sig.
Diabetic cardiomyopathy
PRKCG, COX3, ATP6, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 14 / 205 3.6× 3.45e-5 9.41e-4 ✓ sig.
Amyotrophic lateral sclerosis
ATXN2, COX3, ATP6, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 19 / 368 2.7× 7.13e-5 1.70e-3 ✓ sig.
Anchoring of the basal body to the plasma membrane
TTBK2, DYNC1H1, CSNK1E, RPGRIP1L, TPTEP2-CSNK1E, CEP290, MKS1, TMEM67, TUBA4A
 Reactome 9 / 98 4.9× 9.61e-5 2.18e-3 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
COX3, ATP6, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5, ATP5F1B
 KEGG 14 / 227 3.3× 1.04e-4 2.33e-3 ✓ sig.
Retrograde endocannabinoid signaling
CACNA1A, GRM1, PRKCG, DAGLA, ITPR1, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 11 / 149 3.9× 1.21e-4 2.61e-3 ✓ sig.
Alzheimer disease
MME, ITPR1, COX3, ATP6, ATP8, COX1, COX2, CSNK1E, ND1, ND2, ND3, ND4
 KEGG 19 / 388 2.6× 1.43e-4 2.99e-3 ✓ sig.
Thermogenesis
COX3, ATP6, ATP8, COX1, COX2, ND1, ND2, ND3, ND4, ND4L, ND5, ATP5F1B
 KEGG 13 / 234 2.9× 5.07e-4 8.04e-3 ✓ sig.
Hedgehog 'off' state
KIF7, RPGRIP1L, MKS1, TUBB3, TUBA4A, TUBB6
 Reactome 6 / 56 5.7× 6.29e-4 9.55e-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 ⇵
proton transmembrane transport
COX3, ATP6, ATP6V0A1, ATP8, COX1, COX2, ND1, ND2, ND3, ND4L, SLC36A1, SURF1
 GO:1902600 14 / 181 6.4× 4.72e-8 6.48e-6 ✓ sig.
proton motive force-driven mitochondrial ATP synthesis
ATP6, ATP8, ND1, ND2, ND3, ND4, ND4L, ND5, ATP5F1B
 GO:0042776 9 / 64 11.6× 7.58e-8 9.53e-6 ✓ sig.
aerobic respiration
COX1, MFN2, ND1, ND2, ND3, ND4, ND4L, ND5, SURF1
 GO:0009060 9 / 68 10.9× 1.30e-7 1.50e-5 ✓ sig.
ATP synthesis coupled electron transport
COX2, ND4, ND4L, ND5
 GO:0042773 4 / 7 47.0× 7.21e-7 6.38e-5 ✓ sig.
monoatomic ion transmembrane transport
ANO10, CACNA1A, CACNA1G, GRID2, TRPC3, ITPR1, CLCN2, KCNA6, KCNJ10, KCNN2, SCN8A, ATP2B3
 GO:0034220 18 / 404 3.7× 2.36e-6 1.64e-4 ✓ sig.
respiratory chain complex IV assembly
COX3, SURF1, SLC25A46, COA7
 GO:0008535 4 / 9 36.6× 2.55e-6 1.74e-4 ✓ sig.
mitochondrion organization
AFG3L2, LRRK2, VPS13D, OPA1, PRDX3, MFN2, WDR81, SLC25A46, SPG7, PNPT1
 GO:0007005 10 / 130 6.3× 4.29e-6 2.65e-4 ✓ sig.
monoatomic ion transport
CACNA1A, CACNA1G, GRID2, TRPC3, ITPR1, ATP6, ATP6V0A1, ATP8, CLCN2, KCNA6, KCNJ10, KCNN2
 GO:0006811 23 / 667 2.8× 7.10e-6 3.97e-4 ✓ sig.
glycosphingolipid catabolic process
GBA2, GALC, GLB1, SUMF1
 GO:0046479 4 / 12 27.4× 9.72e-6 5.11e-4 ✓ sig.
regulation of SNARE complex assembly
LRRK2, VPS41, STXBP1, VPS39
 GO:0035542 4 / 12 27.4× 9.72e-6 5.11e-4 ✓ sig.
mitochondrial electron transport, NADH to ubiquinone
ND1, ND2, ND3, ND4, ND4L, ND5
 GO:0006120 6 / 47 10.5× 2.13e-5 9.45e-4 ✓ sig.
protein catabolic process
AFG3L2, MME, TPP1, CLN6, PPT1, SPG11, HSPA8, NQO1
 GO:0030163 8 / 97 6.8× 2.39e-5 1.03e-3 ✓ sig.
regulation of autophagy
LRRK2, EP300, ITPR1, MTCL1, ERCC4, WDR24, ATM
 GO:0010506 7 / 73 7.9× 2.94e-5 1.20e-3 ✓ sig.
action potential
CACNA1G, KCNA6, SCN8A, SCN2A, KCNC3, KCND3
 GO:0001508 6 / 53 9.3× 4.29e-5 1.61e-3 ✓ sig.
chaperone-mediated autophagy
STUB1, HSPA8, ATG5
 GO:0061684 3 / 7 35.3× 5.97e-5 2.05e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cerebellar ataxia Spinocerebellar ataxia 0.210 38 2.79e-56 1.70e-54 ✓ sig.
Cerebellar ataxia Spastic ataxia 0.114 19 3.21e-25 8.38e-24 ✓ sig.
Spastic ataxia Spinocerebellar ataxia 0.074 12 3.61e-14 5.12e-13 ✓ sig.
Spastic ataxia Spastic ataxia optic atrophy dysarthria syndrome 0.014 1 4.55e-3 5.66e-3 ✓ sig.
Spastic ataxia spinocerebellar ataxia type 42 0.014 1 4.55e-3 5.66e-3 ✓ sig.
autosomal recessive cerebellar ataxia Spinocerebellar ataxia 0.010 1 6.75e-3 8.03e-3 ✓ sig.
Spinocerebellar ataxia spinocerebellar ataxia type 13 0.010 1 6.75e-3 8.03e-3 ✓ sig.
Spinocerebellar ataxia spinocerebellar ataxia type 42 0.010 1 6.75e-3 8.03e-3 ✓ sig.
Spinocerebellar ataxia spinocerebellar ataxia, autosomal recessive 23 0.010 1 6.75e-3 8.03e-3 ✓ sig.
Spinocerebellar ataxia spinocerebellar ataxia, autosomal recessive 27 0.010 1 6.75e-3 8.03e-3 ✓ sig.
Spinocerebellar ataxia spinocerebellar ataxia, autosomal recessive 28 0.010 1 6.75e-3 8.03e-3 ✓ sig.
autosomal recessive cerebellar ataxia Cerebellar ataxia 0.009 1 7.40e-3 8.70e-3 ✓ sig.
Cayman type cerebellar ataxia Cerebellar ataxia 0.009 1 7.40e-3 8.70e-3 ✓ sig.
Cerebellar ataxia spinocerebellar ataxia type 42 0.009 1 7.40e-3 8.70e-3 ✓ sig.
Cerebellar ataxia spinocerebellar ataxia, autosomal recessive 23 0.009 1 7.40e-3 8.70e-3 ✓ sig.
3m syndrome Spinocerebellar ataxia 0.009 1 2.01e-2 2.19e-2 ✓ sig.