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 182

10 diseases · 30 shared-gene connections
10 Diseases
6 Unique genes
0.394 Avg. similarity score
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Most-connected disease (8 links)
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Disease Searched: Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation 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 ⇵
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant 8 8 1
Pterygium 8 8 1
Reduced fetal movements 8 8 1
Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 8 8 1
Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 7 7 1
Axonal hereditary motor and sensory neuropathy 5 5 2
Cerebral cortical atrophy 5 5 4
Childhood-onset spinal muscular atrophy 5 5 2
Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 5 5 1
Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
BICD2 9 / 10 Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant, Axonal hereditary motor and sensory neuropathy, Cerebral cortical atrophy, Childhood-onset spinal muscular atrophy and 5 more
DARS2 2 / 10 Cerebral cortical atrophy, Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation
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 ⇵
COPI-independent Golgi-to-ER retrograde traffic
BICD2, DYNC1H1
 Reactome 2 / 51 78.5× 2.62e-4 4.06e-3 ✓ sig.
Signal regulatory protein family interactions
TYROBP
 Reactome 1 / 12 167× 5.98e-3 4.10e-2 ✓ sig.
Other semaphorin interactions
TYROBP
 Reactome 1 / 14 143× 6.98e-3 4.53e-2 ✓ sig.
Mitochondrial tRNA aminoacylation
DARS2
 Reactome 1 / 14 143× 6.98e-3 4.53e-2 ✓ sig.
Processing of SMDT1
SPG7
 Reactome 1 / 16 125× 7.97e-3 4.94e-2 ✓ sig.
DAP12 interactions
TYROBP
 Reactome 1 / 21 95.3× 1.04e-2 5.84e-2
Pink/Parkin Mediated Mitophagy
MFN2
 Reactome 1 / 22 91.0× 1.09e-2 6.01e-2
DAP12 signaling
TYROBP
 Reactome 1 / 30 66.7× 1.49e-2 7.22e-2
Aggrephagy
DYNC1H1
 Reactome 1 / 40 50.0× 1.98e-2 8.52e-2
Neutrophil degranulation
DYNC1H1, TYROBP
 Reactome 2 / 480 8.3× 2.15e-2 8.93e-2
Vasopressin-regulated water reabsorption
DYNC1H1
 KEGG 1 / 44 45.5× 2.18e-2 9.00e-2
HSP90 chaperone cycle for steroid hormone receptors (SHR)
DYNC1H1
 Reactome 1 / 55 36.4× 2.72e-2 1.02e-1
Viral life cycle - HIV-1
BICD2
 KEGG 1 / 64 31.3× 3.16e-2 1.11e-1
Aminoacyl-tRNA biosynthesis
DARS2
 KEGG 1 / 66 30.3× 3.25e-2 1.13e-1
Loss of Nlp from mitotic centrosomes
DYNC1H1
 Reactome 1 / 70 28.6× 3.45e-2 1.17e-1

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-based movement
BICD2, DYNC1H1
 GO:0007018 2 / 87 71.6× 3.18e-4 7.04e-3 ✓ sig.
mitochondrial asparaginyl-tRNA aminoacylation
DARS2
 GO:0070145 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
myeloid leukocyte activation
TYROBP
 GO:0002274 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
positive regulation of cold-induced thermogenesis
DYNC1H1, MFN2
 GO:0120162 2 / 102 61.1× 4.36e-4 8.66e-3 ✓ sig.
aspartyl-tRNA aminoacylation
DARS2
 GO:0006422 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
microtubule anchoring at microtubule organizing center
BICD2
 GO:0072393 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
mitochondrial outer membrane permeabilization involved in programmed cell death
SPG7
 GO:1902686 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
stimulatory killer cell immunoglobulin-like receptor signaling pathway
TYROBP
 GO:0002222 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
mitochondrion organization
MFN2, SPG7
 GO:0007005 2 / 130 47.9× 7.07e-4 1.19e-2 ✓ sig.
regulation of osteoclast development
TYROBP
 GO:2001204 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
regulation of calcium import into the mitochondrion
SPG7
 GO:0110097 1 / 3 1,038× 9.63e-4 1.42e-2 ✓ sig.
minus-end-directed organelle transport along microtubule
BICD2
 GO:0072385 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
positive regulation of microglial cell mediated cytotoxicity
TYROBP
 GO:1904151 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
immune effector process
TYROBP
 GO:0002252 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.
positive regulation of osteoclast development
TYROBP
 GO:2001206 1 / 4 779× 1.28e-3 1.67e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Pterygium 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Reduced fetal movements Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Reduced fetal movements Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Reduced fetal movements Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pterygium Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pterygium Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pterygium Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Pterygium Reduced fetal movements 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Reduced fetal movements 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Childhood-onset spinal muscular atrophy Reduced fetal movements 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Childhood-onset spinal muscular atrophy Pterygium 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Childhood-onset spinal muscular atrophy Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Childhood-onset spinal muscular atrophy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Childhood-onset spinal muscular atrophy Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Axonal hereditary motor and sensory neuropathy Spinal muscular atrophy, lower extremity-predominant 2a, childhood onset, autosomal dominant 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Axonal hereditary motor and sensory neuropathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Axonal hereditary motor and sensory neuropathy Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Axonal hereditary motor and sensory neuropathy Pterygium 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Axonal hereditary motor and sensory neuropathy Reduced fetal movements 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cerebral cortical atrophy Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cerebral cortical atrophy Reduced fetal movements 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Autosomal dominant, spinal muscular atrophy, lower extremity-predominant, 2b, autosomal dominant Cerebral cortical atrophy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cerebral cortical atrophy Spinal muscular atrophy, lower extremity-predominant, 2, autosomal dominant 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cerebral cortical atrophy Pterygium 0.200 1 2.58e-4 5.38e-4 ✓ sig.