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 325

7 diseases · 11 shared-gene connections
7 Diseases
4 Unique genes
0.341 Avg. similarity score
Infantile liver failure Most-connected disease (5 links)
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Disease Searched: Deafness, mitochondrial, modifier of 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 ⇵
Infantile liver failure 5 5 3
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome 4 4 1
Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia 4 4 1
Spinocerebellar ataxia, autosomal recessive 21 4 4 1
Verloes-bourguignon syndrome 3 3 2
Deafness, mitochondrial, modifier of 1 1 1
Infantile-onset recurrent acute liver failure and skeletal abnormalities 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCYL1 5 / 7 Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome, Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia, Infantile liver failure, Spinocerebellar ataxia, autosomal recessive 21 and 1 more
RINT1 2 / 7 Infantile liver failure, Infantile-onset recurrent acute liver failure and skeletal abnormalities
TRMU 2 / 7 Deafness, mitochondrial, modifier of, Infantile liver failure
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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Molecules associated with elastic fibres
LTBP3
 Reactome 1 / 38 79.0× 1.26e-2 6.55e-2
COPI-dependent Golgi-to-ER retrograde traffic
RINT1
 Reactome 1 / 99 30.3× 3.26e-2 1.13e-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 ⇵
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
SCYL1, RINT1
 GO:0006890 2 / 50 187× 4.20e-5 1.61e-3 ✓ sig.
tRNA wobble position uridine thiolation
TRMU
 GO:0002143 1 / 4 1,168× 8.56e-4 1.33e-2 ✓ sig.
positive regulation of mesenchymal stem cell differentiation
LTBP3
 GO:2000741 1 / 5 934× 1.07e-3 1.51e-2 ✓ sig.
lung saccule development
LTBP3
 GO:0060430 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
positive regulation of mesenchymal stem cell proliferation
LTBP3
 GO:1902462 1 / 7 667× 1.50e-3 1.82e-2 ✓ sig.
regulation of ER to Golgi vesicle-mediated transport
RINT1
 GO:0060628 1 / 7 667× 1.50e-3 1.82e-2 ✓ sig.
vesicle-mediated transport
SCYL1, RINT1
 GO:0016192 2 / 326 28.7× 1.78e-3 2.00e-2 ✓ sig.
positive regulation of bone resorption
LTBP3
 GO:0045780 1 / 15 311× 3.21e-3 2.69e-2 ✓ sig.
negative regulation of bone mineralization
LTBP3
 GO:0030502 1 / 17 275× 3.63e-3 2.86e-2 ✓ sig.
bone remodeling
LTBP3
 GO:0046849 1 / 18 260× 3.85e-3 2.94e-2 ✓ sig.
spinal cord motor neuron differentiation
SCYL1
 GO:0021522 1 / 21 222× 4.49e-3 3.17e-2 ✓ sig.
negative regulation of chondrocyte differentiation
LTBP3
 GO:0032331 1 / 23 203× 4.91e-3 3.31e-2 ✓ sig.
bone morphogenesis
LTBP3
 GO:0060349 1 / 32 146× 6.83e-3 3.88e-2 ✓ sig.
mitotic G2 DNA damage checkpoint signaling
RINT1
 GO:0007095 1 / 36 130× 7.68e-3 4.09e-2 ✓ sig.
regulation of cell differentiation
LTBP3
 GO:0045595 1 / 54 86.5× 1.15e-2 4.97e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome Spinocerebellar ataxia, autosomal recessive 21 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia Spinocerebellar ataxia, autosomal recessive 21 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome Verloes-bourguignon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia Verloes-bourguignon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Spinocerebellar ataxia, autosomal recessive 21 Verloes-bourguignon syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome Infantile liver failure 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Deafness, mitochondrial, modifier of Infantile liver failure 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia Infantile liver failure 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Infantile liver failure Spinocerebellar ataxia, autosomal recessive 21 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Infantile liver failure Infantile-onset recurrent acute liver failure and skeletal abnormalities 0.250 1 1.94e-4 4.41e-4 ✓ sig.