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 230

9 diseases · 15 shared-gene connections
9 Diseases
35 Unique genes
0.198 Avg. similarity score
Bilateral perisylvian polymicrogyria Most-connected disease (7 links)
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Disease Searched: Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked 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 ⇵
Bilateral perisylvian polymicrogyria 7 7 3
Perisylvian syndrome 4 4 10
Polymicrogyria 4 4 29
Heparin cofactor 2 deficiency 3 3 3
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis 3 3 1
Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked 3 3 1
Spastic paraplegia 84, autosomal recessive 3 3 1
Bilateral frontoparietal polymicrogyria 2 2 1
Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PI4KA 6 / 9 Bilateral perisylvian polymicrogyria, Heparin cofactor 2 deficiency, Perisylvian syndrome, Polymicrogyria and 2 more
ADGRG1 4 / 9 Bilateral frontoparietal polymicrogyria, Bilateral perisylvian polymicrogyria, Perisylvian syndrome, Polymicrogyria
SRPX2 4 / 9 Bilateral perisylvian polymicrogyria, Perisylvian syndrome, Polymicrogyria, Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked
CCND2 2 / 9 Perisylvian syndrome, Polymicrogyria
SCN3A 2 / 9 Perisylvian syndrome, Polymicrogyria
SHMT2 2 / 9 Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities, Polymicrogyria
TUBB2B 2 / 9 Perisylvian syndrome, Polymicrogyria
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 ⇵
Aggrephagy
TUBA1A, TUBB2B, DYNC1H1, TUBA8
 Reactome 4 / 40 34.3× 5.13e-6 1.68e-4 ✓ sig.
Recruitment of NuMA to mitotic centrosomes
TUBA1A, TUBB2B, DYNC1H1, OFD1, TUBA8
 Reactome 5 / 94 18.3× 7.11e-6 2.20e-4 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic
TUBA1A, TUBB2B, DYNC1H1, TUBA8
 Reactome 4 / 51 26.9× 1.37e-5 3.78e-4 ✓ sig.
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 18 57.2× 1.80e-5 4.76e-4 ✓ sig.
HSP90 chaperone cycle for steroid hormone receptors (SHR)
TUBA1A, TUBB2B, DYNC1H1, TUBA8
 Reactome 4 / 55 25.0× 1.85e-5 4.90e-4 ✓ sig.
Cilium Assembly
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 19 54.2× 2.13e-5 5.48e-4 ✓ sig.
Carboxyterminal post-translational modifications of tubulin
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 27 38.1× 6.32e-5 1.32e-3 ✓ sig.
The role of GTSE1 in G2/M progression after G2 checkpoint
TUBA1A, TUBB2B, PSMC3, TUBA8
 Reactome 4 / 77 17.8× 7.03e-5 1.43e-3 ✓ sig.
MET activates PTK2 signaling
LAMA2, LAMA5, COL3A1
 Reactome 3 / 30 34.3× 8.72e-5 1.70e-3 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 31 33.2× 9.64e-5 1.84e-3 ✓ sig.
RHO GTPases activate IQGAPs
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 32 32.2× 1.06e-4 1.99e-3 ✓ sig.
COPI-mediated anterograde transport
TUBA1A, TUBB2B, DYNC1H1, TUBA8
 Reactome 4 / 101 13.6× 2.02e-4 3.31e-3 ✓ sig.
Separation of Sister Chromatids
TUBA1A, TUBB2B, DYNC1H1, PSMC3, TUBA8
 Reactome 5 / 190 9.0× 2.08e-4 3.38e-3 ✓ sig.
Recycling pathway of L1
TUBA1A, TUBB2B, TUBA8
 Reactome 3 / 40 25.7× 2.08e-4 3.39e-3 ✓ sig.
Mitotic Prometaphase
TUBA1A, TUBB2B, DYNC1H1, TUBA8
 Reactome 4 / 113 12.1× 3.11e-4 4.62e-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 ⇵
cerebral cortex development
TUBA1A, TUBB2B, WDR62, COL3A1
 GO:0021987 4 / 88 24.3× 2.15e-5 9.78e-4 ✓ sig.
positive regulation of cell migration involved in sprouting angiogenesis
SRPX2, NUS1, AKT3
 GO:0090050 3 / 37 43.3× 4.48e-5 1.70e-3 ✓ sig.
response to glycoside
ATP1A2, ATP1A3
 GO:1903416 2 / 6 178× 5.09e-5 1.87e-3 ✓ sig.
microtubule-based process
TUBA1A, TUBB2B, TUBA8
 GO:0007017 3 / 46 34.8× 8.65e-5 2.78e-3 ✓ sig.
regulation of embryonic development
EHMT1, LAMA2, LAMA5
 GO:0045995 3 / 47 34.1× 9.22e-5 2.91e-3 ✓ sig.
neuron migration
TUBA1A, TUBB2B, COL3A1, MAP1B
 GO:0001764 4 / 132 16.2× 1.05e-4 3.21e-3 ✓ sig.
mitotic cell cycle
TUBA1A, TUBB2B, OFD1, TUBA8
 GO:0000278 4 / 142 15.0× 1.39e-4 3.92e-3 ✓ sig.
adult locomotory behavior
CCND2, TUBA1A, ATP1A2
 GO:0008344 3 / 56 28.6× 1.56e-4 4.26e-3 ✓ sig.
microtubule cytoskeleton organization
TUBA1A, TUBB2B, TUBA8, MAP1B
 GO:0000226 4 / 149 14.3× 1.68e-4 4.47e-3 ✓ sig.
establishment or maintenance of transmembrane electrochemical gradient
ATP1A2, ATP1A3
 GO:0010248 2 / 11 97.1× 1.85e-4 4.82e-3 ✓ sig.
cell communication by electrical coupling involved in cardiac conduction
ATP1A2, ATP1A3
 GO:0086064 2 / 12 89.0× 2.22e-4 5.47e-3 ✓ sig.
negative regulation of neuron migration
ADGRG1, COL3A1
 GO:2001223 2 / 12 89.0× 2.22e-4 5.47e-3 ✓ sig.
organelle transport along microtubule
TUBA1A, BORCS5
 GO:0072384 2 / 14 76.3× 3.06e-4 6.87e-3 ✓ sig.
sodium ion export across plasma membrane
ATP1A2, ATP1A3
 GO:0036376 2 / 15 71.2× 3.52e-4 7.52e-3 ✓ sig.
locomotory exploration behavior
TUBA1A, ATP1A2
 GO:0035641 2 / 16 66.7× 4.02e-4 8.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Perisylvian syndrome Polymicrogyria 0.176 6 5.18e-15 6.27e-14 ✓ sig.
Bilateral perisylvian polymicrogyria Perisylvian syndrome 0.273 3 1.94e-10 1.78e-9 ✓ sig.
Bilateral perisylvian polymicrogyria Polymicrogyria 0.100 3 5.90e-9 4.82e-8 ✓ sig.
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis Spastic paraplegia 84, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Bilateral frontoparietal polymicrogyria Bilateral perisylvian polymicrogyria 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria Spastic paraplegia 84, autosomal recessive 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Heparin cofactor 2 deficiency Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Heparin cofactor 2 deficiency Spastic paraplegia 84, autosomal recessive 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bilateral perisylvian polymicrogyria Heparin cofactor 2 deficiency 0.167 1 5.81e-4 1.00e-3 ✓ sig.
Bilateral frontoparietal polymicrogyria Perisylvian syndrome 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Perisylvian syndrome Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities Polymicrogyria 0.033 1 1.87e-3 2.57e-3 ✓ sig.
Polymicrogyria Rolandic epilepsy, impaired intellectual development, and speech dyspraxia, x-linked 0.033 1 1.87e-3 2.57e-3 ✓ sig.