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 33

18 diseases · 48 shared-gene connections
18 Diseases
89 Unique genes
0.293 Avg. similarity score
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Most-connected disease (11 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 ⇵
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 11 11 1
Cerebral small vessel disease 10 10 2
Brain small vessel disease 7 7 5
Colpocephaly 7 7 1
Congenital porencephaly 7 7 2
Posttraumatic porencephalic cyst of brain 7 7 2
Retinal arterial tortuosity 7 7 1
Vascular leukoencephalopathy 7 7 2
COL4A1-related disorder 6 6 1
Cerebral palsy 5 5 46
Intracerebral hemorrhage 5 5 21
Prion disease 5 5 17
Cerebral microangiopathy 4 4 4
Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps 4 4 2
Dementia in huntington’s disease 1 1 2
Ectopic thyroid tissue 1 1 1
Intellectual developmental disorder hypotonia spastic sleep 1 1 1
brain small vessel disease 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL4A1 14 / 18 Brain small vessel disease, Cerebral microangiopathy, Cerebral palsy, Cerebral small vessel disease and 10 more
COL4A2 7 / 18 Brain small vessel disease, Cerebral palsy, Cerebral small vessel disease, Congenital porencephaly and 3 more
ANK3 2 / 18 Intellectual developmental disorder hypotonia spastic sleep, Prion disease
COLGALT1 2 / 18 Brain small vessel disease, brain small vessel disease 3
FBXO31 2 / 18 Cerebral palsy, Ectopic thyroid tissue
PRNP 2 / 18 Dementia in huntington’s disease, Prion disease
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 ⇵
Crosslinking of collagen fibrils
COL4A1, COL4A2, LOXL2
 Reactome 3 / 18 22.5× 2.96e-4 5.31e-3 ✓ sig.
Synthesis of Leukotrienes (LT) and Eoxins (EX)
ALOX5AP, CYP4F3, CYP4F8
 Reactome 3 / 20 20.2× 4.09e-4 6.83e-3 ✓ sig.
GABAergic synapse
CACNA1A, CACNA1C, GNB1, GPHN, GAD1
 KEGG 5 / 89 7.6× 5.08e-4 8.05e-3 ✓ sig.
Mitotic Prometaphase
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 113 6.0× 1.49e-3 1.84e-2 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL4A1, COL4A2, COLGALT1, ADAMTS14
 Reactome 4 / 67 8.1× 1.51e-3 1.86e-2 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III
SPAST, TUBA1A, TUBB4A
 Reactome 3 / 31 13.1× 1.52e-3 1.87e-2 ✓ sig.
EML4 and NUDC in mitotic spindle formation
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 117 5.8× 1.74e-3 2.06e-2 ✓ sig.
Signaling by PDGF
COL4A1, COL4A2, PDGFRB
 Reactome 3 / 33 12.3× 1.83e-3 2.14e-2 ✓ sig.
Resolution of Sister Chromatid Cohesion
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 126 5.4× 2.41e-3 2.62e-2 ✓ sig.
Eicosanoids
CYP4F3, CYP4F8
 Reactome 2 / 12 22.5× 3.42e-3 3.38e-2 ✓ sig.
RHO GTPases Activate Formins
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 140 4.8× 3.80e-3 3.64e-2 ✓ sig.
Focal adhesion
COL4A1, COL4A2, EGFR, PDGFRB, MYL2, PARVB
 KEGG 6 / 203 4.0× 3.93e-3 3.73e-2 ✓ sig.
Gap junction
EGFR, PDGFRB, TUBA1A, TUBB4A
 KEGG 4 / 89 6.1× 4.26e-3 3.94e-2 ✓ sig.
Fatty acids
CYP4F3, CYP4F8
 Reactome 2 / 15 18.0× 5.36e-3 4.58e-2 ✓ sig.
Extracellular matrix organization
COL4A1, COL4A2
 Reactome 2 / 15 18.0× 5.36e-3 4.58e-2 ✓ 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 ⇵
response to copper ion
LOXL2, PRNP, SOD1
 GO:0046688 3 / 12 52.5× 2.23e-5 9.76e-4 ✓ sig.
cardiac myofibril assembly
PDGFRB, TTN, MYL2
 GO:0055003 3 / 13 48.5× 2.89e-5 1.19e-3 ✓ sig.
heart contraction
ACE, MYL2, SOD1
 GO:0060047 3 / 23 27.4× 1.73e-4 4.54e-3 ✓ sig.
menaquinone catabolic process
CYP4F3, CYP4F8
 GO:0042361 2 / 5 84.0× 2.22e-4 5.43e-3 ✓ sig.
negative regulation of dendritic spine maintenance
GRIN2B, PRNP
 GO:1902951 2 / 6 70.0× 3.32e-4 7.20e-3 ✓ sig.
regulation of viral entry into host cell
NECTIN2, TRIM5
 GO:0046596 2 / 6 70.0× 3.32e-4 7.20e-3 ✓ sig.
phylloquinone catabolic process
CYP4F3, CYP4F8
 GO:0042376 2 / 6 70.0× 3.32e-4 7.20e-3 ✓ sig.
peripheral nervous system myelin maintenance
PALS1, SOD1
 GO:0032287 2 / 9 46.7× 7.90e-4 1.30e-2 ✓ sig.
cerebral cortex cell migration
EGFR, DAB1
 GO:0021795 2 / 11 38.2× 1.20e-3 1.69e-2 ✓ sig.
telomere maintenance via recombination
BRCA2, TEP1
 GO:0000722 2 / 11 38.2× 1.20e-3 1.69e-2 ✓ sig.
icosanoid metabolic process
CYP4F3, CYP4F8
 GO:0006690 2 / 11 38.2× 1.20e-3 1.69e-2 ✓ sig.
microtubule-based process
HTT, TUBA1A, TUBB4A
 GO:0007017 3 / 46 13.7× 1.37e-3 1.82e-2 ✓ sig.
collagen-activated tyrosine kinase receptor signaling pathway
COL4A1, COL4A2
 GO:0038063 2 / 12 35.0× 1.44e-3 1.87e-2 ✓ sig.
calcium ion transport into cytosol
CACNA1C, JPH3
 GO:0060402 2 / 14 30.0× 1.97e-3 2.24e-2 ✓ sig.
response to amyloid-beta
CACNA1A, PRNP
 GO:1904645 2 / 15 28.0× 2.26e-3 2.42e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Posttraumatic porencephalic cyst of brain Vascular leukoencephalopathy 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Congenital porencephaly Vascular leukoencephalopathy 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Congenital porencephaly Posttraumatic porencephalic cyst of brain 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Cerebral small vessel disease Posttraumatic porencephalic cyst of brain 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Cerebral small vessel disease Congenital porencephaly 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Cerebral small vessel disease Vascular leukoencephalopathy 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Brain small vessel disease Vascular leukoencephalopathy 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Brain small vessel disease Congenital porencephaly 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Brain small vessel disease Posttraumatic porencephalic cyst of brain 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Brain small vessel disease Cerebral small vessel disease 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Intracerebral hemorrhage Posttraumatic porencephalic cyst of brain 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Congenital porencephaly Intracerebral hemorrhage 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Intracerebral hemorrhage Vascular leukoencephalopathy 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Cerebral small vessel disease Intracerebral hemorrhage 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Cerebral palsy Vascular leukoencephalopathy 0.043 2 8.73e-6 4.59e-5 ✓ sig.
Cerebral palsy Posttraumatic porencephalic cyst of brain 0.043 2 8.73e-6 4.59e-5 ✓ sig.
Cerebral palsy Congenital porencephaly 0.043 2 8.73e-6 4.59e-5 ✓ sig.
Cerebral palsy Cerebral small vessel disease 0.043 2 8.73e-6 4.59e-5 ✓ sig.
Brain small vessel disease Intracerebral hemorrhage 0.080 2 1.77e-5 8.93e-5 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Retinal arterial tortuosity 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Colpocephaly Retinal arterial tortuosity 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Colpocephaly Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL4A1-related disorder Retinal arterial tortuosity 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL4A1-related disorder Colpocephaly 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL4A1-related disorder Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL4A1-related disorder Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Vascular leukoencephalopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral small vessel disease Retinal arterial tortuosity 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Posttraumatic porencephalic cyst of brain 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps Retinal arterial tortuosity 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral small vessel disease Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital porencephaly Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral small vessel disease Colpocephaly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Colpocephaly Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral small vessel disease COL4A1-related disorder 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral microangiopathy COL4A1-related disorder 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cerebral microangiopathy Retinal arterial tortuosity 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cerebral microangiopathy Colpocephaly 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cerebral microangiopathy Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Brain small vessel disease brain small vessel disease 3 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Brain small vessel disease Familial hematuria-retinal arteriolar tortuosity-contractures syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Intellectual developmental disorder hypotonia spastic sleep Prion disease 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome Prion disease 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Colpocephaly Prion disease 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Prion disease Retinal arterial tortuosity 0.056 1 1.10e-3 1.81e-3 ✓ sig.
Dementia in huntington’s disease Prion disease 0.053 1 2.21e-3 3.10e-3 ✓ sig.
Cerebral palsy Ectopic thyroid tissue 0.021 1 2.99e-3 3.94e-3 ✓ sig.