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 190

9 diseases · 18 shared-gene connections
9 Diseases
51 Unique genes
0.148 Avg. similarity score
Complex cortical dysplasia with other brain malformations Most-connected disease (7 links)
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Disease Searched: Lissencephaly spectrum disorders 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 ⇵
Complex cortical dysplasia with other brain malformations 7 7 14
Cortical dysplasia with other brain malformations 7 7 17
Cortical development malformation 5 5 27
Congenital fibrosis of extraocular muscles 4 4 16
Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures 4 4 1
Lissencephaly spectrum disorders 3 3 4
Tubulinopathy 3 3 4
Neuronal migration disorder 2 2 1
Goldberg-Shprintzen syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TUBB2B 5 / 9 Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical development malformation, Cortical dysplasia with other brain malformations and 1 more
TUBGCP2 5 / 9 Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations, Lissencephaly spectrum disorders and 1 more
TUBB3 4 / 9 Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical dysplasia with other brain malformations, Tubulinopathy
TUBG1 4 / 9 Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations, Lissencephaly spectrum disorders
APC2 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations, Lissencephaly spectrum disorders
CAMSAP1 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations, Neuronal migration disorder
DYNC1H1 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations
KIF2A 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations
KIF5C 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations
TUBA1A 3 / 9 Congenital fibrosis of extraocular muscles, Cortical development malformation, Tubulinopathy
TUBB 3 / 9 Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical dysplasia with other brain malformations
TUBB2A 3 / 9 Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations, Tubulinopathy
CTNNA2 2 / 9 Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations
HRAS 2 / 9 Congenital fibrosis of extraocular muscles, Cortical development malformation
KIF26A 2 / 9 Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations
KIFBP 2 / 9 Cortical development malformation, Goldberg-Shprintzen syndrome
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 ⇵
Motor proteins
KIF26A, TUBB2B, TUBB3, KIF5C, KIF2A, TUBG1, TUBB2A, TUBB, KIF21A, TUBA1A, MYH10, TUBA1B
 KEGG 14 / 194 17.0× 3.94e-14 1.01e-11 ✓ sig.
Cilium Assembly
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, HDAC6, TUBA8
 Reactome 7 / 19 86.8× 7.86e-13 1.55e-10 ✓ sig.
Kinesins
KIF26A, TUBB2B, TUBB3, KIF2A, TUBB2A, KIF21A, TUBA1A, TUBA1B, TUBA8
 Reactome 9 / 59 35.9× 2.29e-12 4.02e-10 ✓ sig.
Aggrephagy
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, DYNC1H1, HDAC6, TUBA8
 Reactome 8 / 40 47.1× 4.13e-12 6.86e-10 ✓ sig.
Recruitment of NuMA to mitotic centrosomes
TUBB2B, TUBB3, TUBG1, TUBB2A, TUBB, TUBA1A, TUBA1B, DYNC1H1, TUBGCP2, TUBA8
 Reactome 10 / 94 25.1× 5.19e-12 8.41e-10 ✓ sig.
RHO GTPases activate IQGAPs
TUBB2B, TUBB3, TUBB2A, TUBA1A, CTNNA1, TUBA1B, TUBA8
 Reactome 7 / 32 51.5× 5.04e-11 6.41e-9 ✓ sig.
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, TUBA8
 Reactome 6 / 18 78.5× 7.73e-11 9.31e-9 ✓ sig.
COPI-dependent Golgi-to-ER retrograde traffic
KIF26A, TUBB2B, TUBB3, KIF2A, TUBB2A, KIF21A, TUBA1A, TUBA1B, TUBA8
 Reactome 9 / 99 21.4× 2.77e-10 2.94e-8 ✓ sig.
Salmonella infection
TUBB2B, TUBB3, KIF5C, TUBB2A, TUBB, TUBA1A, HRAS, TUBA1B, DYNC1H1, AKT3, PIK3CA, TUBA8
 KEGG 12 / 248 11.4× 3.58e-10 3.71e-8 ✓ sig.
Carboxyterminal post-translational modifications of tubulin
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, TUBA8
 Reactome 6 / 27 52.3× 1.20e-9 1.09e-7 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, DYNC1H1, TUBA8
 Reactome 7 / 51 32.3× 1.63e-9 1.44e-7 ✓ sig.
MHC class II antigen presentation
KIF26A, TUBB2B, TUBB3, KIF2A, TUBB2A, TUBA1A, TUBA1B, DYNC1H1, TUBA8
 Reactome 9 / 123 17.2× 1.95e-9 1.69e-7 ✓ sig.
HSP90 chaperone cycle for steroid hormone receptors (SHR)
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, DYNC1H1, TUBA8
 Reactome 7 / 55 30.0× 2.82e-9 2.38e-7 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III
TUBB2B, TUBB3, TUBB2A, TUBA1A, TUBA1B, TUBA8
 Reactome 6 / 31 45.6× 2.94e-9 2.47e-7 ✓ sig.
Gap junction
TUBB2B, TUBB3, TUBB2A, TUBB, TUBA1A, HRAS, TUBA1B, TUBA8
 KEGG 8 / 89 21.2× 3.24e-9 2.70e-7 ✓ 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 ⇵
microtubule cytoskeleton organization
TUBB2B, TUBB3, KIF2A, TUBG1, TUBB2A, TUBB, TUBA1A, TUBA1B, APC2, CAMSAP1, TUBGCP2, KIFBP
 GO:0000226 14 / 149 34.4× 2.26e-18 2.85e-15 ✓ sig.
microtubule-based process
TUBB2B, TUBB3, TUBG1, TUBB2A, TUBB, TUBA1A, TUBA1B, TUBA8
 GO:0007017 8 / 46 63.7× 4.17e-13 2.11e-10 ✓ sig.
mitotic cell cycle
TUBB2B, TUBB3, TUBG1, TUBB2A, TUBB, TUBA1A, TUBA1B, TUBGCP2, TBCD, TUBA8
 GO:0000278 10 / 142 25.8× 4.56e-12 1.88e-9 ✓ sig.
neuron migration
TUBB2B, TUBB2A, TUBA1A, MYH10, TUBGCP2, DCX
 GO:0001764 6 / 132 16.7× 1.54e-6 1.23e-4 ✓ sig.
microtubule-based movement
KIF26A, KIF5C, KIF2A, KIF21A, DYNC1H1
 GO:0007018 5 / 87 21.1× 3.86e-6 2.57e-4 ✓ sig.
cerebral cortex development
KIF26A, TUBB2B, TUBB2A, TUBA1A, WDR62
 GO:0021987 5 / 88 20.8× 4.09e-6 2.70e-4 ✓ sig.
brain development
GRHL2, MYH10, NES, ADGRG1, TUBGCP2, SLC1A1, DHX37
 GO:0007420 7 / 244 10.5× 4.21e-6 2.76e-4 ✓ sig.
cytoskeleton-dependent intracellular transport
TUBB, TUBA1A, TUBA1B
 GO:0030705 3 / 14 78.5× 6.82e-6 4.04e-4 ✓ sig.
mitotic spindle organization
KIF2A, TUBG1, DYNC1H1, WDR62
 GO:0007052 4 / 58 25.3× 1.87e-5 8.78e-4 ✓ sig.
insulin receptor signaling pathway
HRAS, AKT3, MTOR, PIK3CA
 GO:0008286 4 / 80 18.3× 6.68e-5 2.29e-3 ✓ sig.
neuron apoptotic process
TUBA1A, HRAS, NES, SLC1A1
 GO:0051402 4 / 98 15.0× 1.47e-4 4.08e-3 ✓ sig.
neurogenesis
TUBA1A, FGF21, SLC1A1, WDR62
 GO:0022008 4 / 102 14.4× 1.72e-4 4.55e-3 ✓ sig.
cytoplasmic microtubule organization
TUBG1, DYNC1H1, TUBGCP2
 GO:0031122 3 / 46 23.9× 2.68e-4 6.25e-3 ✓ sig.
nervous system development
TUBB2B, KIF2A, NES, APC2, ADGRG1, KIFBP, WDR62, DCX
 GO:0007399 8 / 631 4.6× 2.85e-4 6.55e-3 ✓ sig.
intracellular mRNA localization
KIF5C, METTL1
 GO:0008298 2 / 10 73.3× 3.24e-4 7.08e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Complex cortical dysplasia with other brain malformations Cortical dysplasia with other brain malformations 0.684 13 7.07e-41 1.68e-39 ✓ sig.
Complex cortical dysplasia with other brain malformations Cortical development malformation 0.171 6 3.58e-14 4.16e-13 ✓ sig.
Cortical development malformation Cortical dysplasia with other brain malformations 0.158 6 1.47e-13 1.65e-12 ✓ sig.
Complex cortical dysplasia with other brain malformations Lissencephaly spectrum disorders 0.188 3 2.35e-9 1.97e-8 ✓ sig.
Complex cortical dysplasia with other brain malformations Tubulinopathy 0.188 3 2.35e-9 1.97e-8 ✓ sig.
Congenital fibrosis of extraocular muscles Tubulinopathy 0.167 3 3.62e-9 2.99e-8 ✓ sig.
Cortical dysplasia with other brain malformations Lissencephaly spectrum disorders 0.158 3 4.39e-9 3.62e-8 ✓ sig.
Cortical dysplasia with other brain malformations Tubulinopathy 0.158 3 4.39e-9 3.62e-8 ✓ sig.
Complex cortical dysplasia with other brain malformations Congenital fibrosis of extraocular muscles 0.107 3 3.27e-7 2.13e-6 ✓ sig.
Congenital fibrosis of extraocular muscles Cortical dysplasia with other brain malformations 0.097 3 6.10e-7 3.82e-6 ✓ sig.
Congenital fibrosis of extraocular muscles Cortical development malformation 0.075 3 2.32e-6 1.34e-5 ✓ sig.
Lissencephaly spectrum disorders Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Complex cortical dysplasia with other brain malformations Neuronal migration disorder 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Complex cortical dysplasia with other brain malformations Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Cortical dysplasia with other brain malformations Neuronal migration disorder 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Cortical dysplasia with other brain malformations Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Cortical development malformation Goldberg-Shprintzen syndrome 0.037 1 1.68e-3 2.34e-3 ✓ sig.
Cortical development malformation Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures 0.037 1 1.68e-3 2.34e-3 ✓ sig.