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 192

8 diseases · 20 shared-gene connections
8 Diseases
68 Unique genes
0.298 Avg. similarity score
Cerebral small vessel disease Most-connected disease (6 links)
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Disease Searched: Brain small vessel 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 ⇵
Cerebral small vessel disease 6 6 2
Congenital porencephaly 6 6 2
Posttraumatic porencephalic cyst of brain 6 6 2
Vascular leukoencephalopathy 6 6 2
Brain small vessel disease 5 5 5
Cerebral palsy 5 5 46
Intracerebral hemorrhage 5 5 21
Ectopic thyroid tissue 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL4A1 7 / 8 Brain small vessel disease, Cerebral palsy, Cerebral small vessel disease, Congenital porencephaly and 3 more
COL4A2 7 / 8 Brain small vessel disease, Cerebral palsy, Cerebral small vessel disease, Congenital porencephaly and 3 more
FBXO31 2 / 8 Cerebral palsy, Ectopic thyroid tissue
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 29.4× 1.33e-4 2.75e-3 ✓ sig.
GABAergic synapse
CACNA1A, CACNA1C, GNB1, GPHN, GAD1
 KEGG 5 / 89 9.9× 1.44e-4 2.93e-3 ✓ sig.
Synthesis of Leukotrienes (LT) and Eoxins (EX)
ALOX5AP, CYP4F3, CYP4F8
 Reactome 3 / 20 26.5× 1.85e-4 3.57e-3 ✓ sig.
Mitotic Prometaphase
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 113 7.8× 4.39e-4 7.11e-3 ✓ sig.
EML4 and NUDC in mitotic spindle formation
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 117 7.5× 5.15e-4 8.04e-3 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III
SPAST, TUBA1A, TUBB4A
 Reactome 3 / 31 17.1× 6.97e-4 1.02e-2 ✓ sig.
Resolution of Sister Chromatid Cohesion
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 126 7.0× 7.21e-4 1.05e-2 ✓ sig.
Signaling by PDGF
COL4A1, COL4A2, PDGFRB
 Reactome 3 / 33 16.1× 8.39e-4 1.17e-2 ✓ sig.
Focal adhesion
COL4A1, COL4A2, EGFR, PDGFRB, MYL2, PARVB
 KEGG 6 / 203 5.2× 9.92e-4 1.33e-2 ✓ sig.
RHO GTPases Activate Formins
BUB1B, TUBA1A, TUBB4A, PMF1, PMF1-BGLAP
 Reactome 5 / 140 6.3× 1.16e-3 1.51e-2 ✓ sig.
Gap junction
EGFR, PDGFRB, TUBA1A, TUBB4A
 KEGG 4 / 89 7.9× 1.60e-3 1.93e-2 ✓ sig.
Eicosanoids
CYP4F3, CYP4F8
 Reactome 2 / 12 29.4× 2.01e-3 2.29e-2 ✓ sig.
Hypertrophic cardiomyopathy
CACNA1C, TTN, ACE, MYL2
 KEGG 4 / 99 7.1× 2.36e-3 2.57e-2 ✓ sig.
Fatty acids
CYP4F3, CYP4F8
 Reactome 2 / 15 23.5× 3.16e-3 3.18e-2 ✓ sig.
Extracellular matrix organization
COL4A1, COL4A2
 Reactome 2 / 15 23.5× 3.16e-3 3.18e-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 ⇵
cardiac myofibril assembly
PDGFRB, TTN, MYL2
 GO:0055003 3 / 13 63.4× 1.28e-5 6.38e-4 ✓ sig.
menaquinone catabolic process
CYP4F3, CYP4F8
 GO:0042361 2 / 5 110× 1.30e-4 3.69e-3 ✓ sig.
regulation of viral entry into host cell
NECTIN2, TRIM5
 GO:0046596 2 / 6 91.6× 1.94e-4 4.94e-3 ✓ sig.
phylloquinone catabolic process
CYP4F3, CYP4F8
 GO:0042376 2 / 6 91.6× 1.94e-4 4.94e-3 ✓ sig.
microtubule-based process
HTT, TUBA1A, TUBB4A
 GO:0007017 3 / 46 17.9× 6.25e-4 1.12e-2 ✓ sig.
cerebral cortex cell migration
EGFR, DAB1
 GO:0021795 2 / 11 50.0× 7.03e-4 1.21e-2 ✓ sig.
telomere maintenance via recombination
BRCA2, TEP1
 GO:0000722 2 / 11 50.0× 7.03e-4 1.21e-2 ✓ sig.
icosanoid metabolic process
CYP4F3, CYP4F8
 GO:0006690 2 / 11 50.0× 7.03e-4 1.21e-2 ✓ sig.
collagen-activated tyrosine kinase receptor signaling pathway
COL4A1, COL4A2
 GO:0038063 2 / 12 45.8× 8.41e-4 1.36e-2 ✓ sig.
positive regulation of miRNA transcription
EGFR, SMARCA4, NOTCH3
 GO:1902895 3 / 56 14.7× 1.11e-3 1.62e-2 ✓ sig.
regulation of DNA damage checkpoint
BRCA2, RNASEH2B
 GO:2000001 2 / 15 36.6× 1.33e-3 1.81e-2 ✓ sig.
locomotory exploration behavior
TUBA1A, GAD1
 GO:0035641 2 / 16 34.4× 1.51e-3 1.95e-2 ✓ sig.
layer formation in cerebral cortex
ADGRG1, DAB1
 GO:0021819 2 / 18 30.5× 1.92e-3 2.23e-2 ✓ sig.
leukotriene metabolic process
ALOX5AP, CYP4F3
 GO:0006691 2 / 18 30.5× 1.92e-3 2.23e-2 ✓ sig.
positive regulation of peptidyl-serine phosphorylation
EGFR, TENM1
 GO:0033138 2 / 20 27.5× 2.38e-3 2.54e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cerebral small vessel disease Posttraumatic porencephalic cyst of brain 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Posttraumatic porencephalic cyst of brain Vascular leukoencephalopathy 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Congenital porencephaly Posttraumatic porencephalic cyst of brain 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Congenital porencephaly Vascular leukoencephalopathy 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Cerebral small vessel disease Congenital porencephaly 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Cerebral small vessel disease Vascular leukoencephalopathy 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Brain small vessel disease Cerebral small vessel disease 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Brain small vessel disease Posttraumatic porencephalic cyst of brain 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Brain small vessel disease Congenital porencephaly 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Brain small vessel disease Vascular leukoencephalopathy 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Cerebral small vessel disease Intracerebral hemorrhage 0.091 2 1.77e-6 9.96e-6 ✓ sig.
Intracerebral hemorrhage Vascular leukoencephalopathy 0.091 2 1.77e-6 9.96e-6 ✓ sig.
Congenital porencephaly Intracerebral hemorrhage 0.091 2 1.77e-6 9.96e-6 ✓ sig.
Intracerebral hemorrhage Posttraumatic porencephalic cyst of brain 0.091 2 1.77e-6 9.96e-6 ✓ sig.
Cerebral palsy Congenital porencephaly 0.043 2 8.73e-6 4.34e-5 ✓ sig.
Cerebral palsy Posttraumatic porencephalic cyst of brain 0.043 2 8.73e-6 4.34e-5 ✓ sig.
Cerebral palsy Vascular leukoencephalopathy 0.043 2 8.73e-6 4.34e-5 ✓ sig.
Cerebral palsy Cerebral small vessel disease 0.043 2 8.73e-6 4.34e-5 ✓ sig.
Brain small vessel disease Intracerebral hemorrhage 0.080 2 1.77e-5 8.44e-5 ✓ sig.
Cerebral palsy Ectopic thyroid tissue 0.021 1 2.99e-3 3.95e-3 ✓ sig.