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 172

9 diseases · 22 shared-gene connections
9 Diseases
44 Unique genes
0.164 Avg. similarity score
Dystonia 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 ⇵
Dystonia 8 8 44
Dystonia musculorum deformans 7 7 9
Genetic torsion dystonia 7 7 9
Torsion dystonia 6 6 7
Early-onset generalized limb-onset dystonia 4 4 3
complex movement disorder with or without neurodevelopmental features 4 4 1
Focal dystonia 3 3 1
X-linked dystonia-parkinsonism 3 3 1
Cervical dystonia 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HPCA 5 / 9 complex movement disorder with or without neurodevelopmental features, Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia and 1 more
TOR1A 5 / 9 Dystonia, Dystonia musculorum deformans, Early-onset generalized limb-onset dystonia, Genetic torsion dystonia and 1 more
GNAL 4 / 9 Dystonia, Dystonia musculorum deformans, Focal dystonia, Genetic torsion dystonia
TAF1 4 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia, X-linked dystonia-parkinsonism
THAP1 4 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia, Torsion dystonia
TUBB4A 4 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia, Torsion dystonia
CIZ1 3 / 9 Cervical dystonia, Dystonia, Torsion dystonia
COL6A3 3 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia
EIF2AK2 3 / 9 Dystonia, Early-onset generalized limb-onset dystonia, Torsion dystonia
GCH1 3 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia
SGCE 3 / 9 Dystonia, Dystonia musculorum deformans, Genetic torsion dystonia
SHQ1 3 / 9 Dystonia, Early-onset generalized limb-onset dystonia, Torsion dystonia
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 ⇵
Folate biosynthesis
GCH1, TH, SPR
 KEGG 3 / 28 29.2× 1.41e-4 2.96e-3 ✓ sig.
Efferocytosis
ANO3, PLA2G6, SLC2A1, VPS16, VPS11
 KEGG 5 / 157 8.7× 2.58e-4 4.76e-3 ✓ sig.
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
GCH1, SPR
 Reactome 2 / 11 49.6× 7.07e-4 1.04e-2 ✓ sig.
Inhibition of PKR
EIF2AK2
 Reactome 1 / 1 273× 3.66e-3 3.54e-2 ✓ sig.
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)
SLC2A1
 Reactome 1 / 1 273× 3.66e-3 3.54e-2 ✓ sig.
Insulin secretion
ATP1A3, SLC2A1, KCNN2
 KEGG 3 / 86 9.5× 3.80e-3 3.64e-2 ✓ sig.
Bile secretion
ATP1A3, SLC2A1, KCNN2
 KEGG 3 / 90 9.1× 4.32e-3 3.98e-2 ✓ sig.
RHO GTPases activate IQGAPs
ACTB, TUBB4A
 Reactome 2 / 32 17.1× 6.07e-3 4.97e-2 ✓ sig.
Degradation of GABA
ALDH5A1
 Reactome 1 / 2 136× 7.31e-3 5.62e-2
Serotonergic synapse
CYP2D6, CACNA1B, KCNN2
 KEGG 3 / 115 7.1× 8.52e-3 6.22e-2
Recycling pathway of L1
ACTB, TUBB4A
 Reactome 2 / 40 13.6× 9.37e-3 6.59e-2
Nicotine addiction
CHRNA4, CACNA1B
 KEGG 2 / 41 13.3× 9.82e-3 6.79e-2
Thyroid hormone signaling pathway
ACTB, ATP1A3, SLC2A1
 KEGG 3 / 122 6.7× 1.00e-2 6.84e-2
Cytoskeleton in muscle cells
ACTB, ATP1A3, COL6A3, SGCE
 KEGG 4 / 232 4.7× 1.01e-2 6.87e-2
Lactose synthesis
SLC2A1
 Reactome 1 / 3 91.0× 1.10e-2 7.25e-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 ⇵
neuromuscular process controlling posture
GCH1, PRRT2, GLRA1
 GO:0050884 3 / 15 84.9× 5.43e-6 3.21e-4 ✓ sig.
tetrahydrobiopterin biosynthetic process
GCH1, SPR
 GO:0006729 2 / 8 106× 1.50e-4 4.10e-3 ✓ sig.
dopamine biosynthetic process
GCH1, TH
 GO:0042416 2 / 9 94.4× 1.93e-4 4.93e-3 ✓ sig.
inhibitory postsynaptic potential
CHRNA4, GLRA1
 GO:0060080 2 / 10 84.9× 2.41e-4 5.77e-3 ✓ sig.
monoatomic ion transmembrane transport
ANO3, CHRNA4, SCN2A, CACNA1B, KCNN2, GLRA1
 GO:0034220 6 / 404 6.3× 3.47e-4 7.42e-3 ✓ sig.
regulation of SNARE complex assembly
VPS16, VPS11
 GO:0035542 2 / 12 70.8× 3.52e-4 7.48e-3 ✓ sig.
intracellular cholesterol transport
SCP2, SERAC1
 GO:0032367 2 / 13 65.3× 4.16e-4 8.44e-3 ✓ sig.
vacuole organization
VPS16, VPS11
 GO:0007033 2 / 13 65.3× 4.16e-4 8.44e-3 ✓ sig.
endosomal vesicle fusion
VPS16, VPS11
 GO:0034058 2 / 15 56.6× 5.58e-4 1.03e-2 ✓ sig.
response to hypoxia
CHRNA4, TH, SLC2A1, ND1
 GO:0001666 4 / 176 9.7× 7.69e-4 1.27e-2 ✓ sig.
monoatomic ion transport
ATP1A3, CHRNA4, SLC30A10, SCN2A, CACNA1B, KCNN2, GLRA1
 GO:0006811 7 / 667 4.5× 8.67e-4 1.37e-2 ✓ sig.
nitric oxide biosynthetic process
GCH1, SPR
 GO:0006809 2 / 23 36.9× 1.33e-3 1.79e-2 ✓ sig.
positive regulation of norepinephrine uptake
ACTB
 GO:0051623 1 / 1 425× 2.35e-3 2.48e-2 ✓ sig.
cellular response to cytochalasin B
ACTB
 GO:0072749 1 / 1 425× 2.35e-3 2.48e-2 ✓ sig.
pteridine-containing compound biosynthetic process
GCH1
 GO:0042559 1 / 1 425× 2.35e-3 2.48e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Dystonia musculorum deformans Genetic torsion dystonia 0.900 9 7.47e-33 2.66e-31 ✓ sig.
Dystonia Dystonia musculorum deformans 0.200 9 5.30e-24 1.29e-22 ✓ sig.
Dystonia Genetic torsion dystonia 0.200 9 5.30e-24 1.29e-22 ✓ sig.
Dystonia Torsion dystonia 0.156 7 9.42e-19 1.77e-17 ✓ sig.
Genetic torsion dystonia Torsion dystonia 0.308 4 1.88e-12 2.31e-11 ✓ sig.
Dystonia musculorum deformans Torsion dystonia 0.308 4 1.88e-12 2.31e-11 ✓ sig.
Early-onset generalized limb-onset dystonia Torsion dystonia 0.375 3 5.75e-11 6.20e-10 ✓ sig.
Dystonia Early-onset generalized limb-onset dystonia 0.067 3 2.18e-8 1.79e-7 ✓ sig.
complex movement disorder with or without neurodevelopmental features Torsion dystonia 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Cervical dystonia Torsion dystonia 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Genetic torsion dystonia X-linked dystonia-parkinsonism 0.100 1 5.84e-4 1.14e-3 ✓ sig.
complex movement disorder with or without neurodevelopmental features Genetic torsion dystonia 0.100 1 5.84e-4 1.14e-3 ✓ sig.
complex movement disorder with or without neurodevelopmental features Dystonia musculorum deformans 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Dystonia musculorum deformans Focal dystonia 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Focal dystonia Genetic torsion dystonia 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Dystonia musculorum deformans X-linked dystonia-parkinsonism 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Dystonia musculorum deformans Early-onset generalized limb-onset dystonia 0.083 1 1.75e-3 2.59e-3 ✓ sig.
Early-onset generalized limb-onset dystonia Genetic torsion dystonia 0.083 1 1.75e-3 2.59e-3 ✓ sig.
Dystonia X-linked dystonia-parkinsonism 0.022 1 2.86e-3 3.80e-3 ✓ sig.
Dystonia Focal dystonia 0.022 1 2.86e-3 3.80e-3 ✓ sig.
complex movement disorder with or without neurodevelopmental features Dystonia 0.022 1 2.86e-3 3.80e-3 ✓ sig.
Cervical dystonia Dystonia 0.022 1 2.86e-3 3.80e-3 ✓ sig.