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 187

10 diseases · 31 shared-gene connections
10 Diseases
2 Unique genes
0.468 Avg. similarity score
Cutis laxa, autosomal recessive, 3a Most-connected disease (8 links)
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Disease Searched: Spastic paraplegia 9b, autosomal recessive 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 ⇵
Cutis laxa, autosomal recessive, 3a 8 8 1
Cutis laxa, corneal clouding, and mental retardation 8 8 1
De barsy syndrome 8 8 1
Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 8 8 1
P5CS deficiency 8 8 1
Complex spastic paraplegia 6 6 2
Cutis laxa, autosomal dominant 3 5 5 1
Spastic paraplegia 9 5 5 1
Spastic paraplegia 9b, autosomal recessive 5 5 1
Spastic paraplegia 81, autosomal recessive 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ALDH18A1 9 / 10 Complex spastic paraplegia, Cutis laxa, autosomal dominant 3, Cutis laxa, autosomal recessive, 3a, Cutis laxa, corneal clouding, and mental retardation and 5 more
SELENOI 2 / 10 Complex spastic paraplegia, Spastic paraplegia 81, autosomal recessive
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 ⇵
Phosphonate and phosphinate metabolism
SELENOI
 KEGG 1 / 6 1,001× 9.99e-4 1.13e-2 ✓ sig.
Synthesis of PE
SELENOI
 Reactome 1 / 12 500× 2.00e-3 1.90e-2 ✓ sig.
Glutamate and glutamine metabolism
ALDH18A1
 Reactome 1 / 14 429× 2.33e-3 2.13e-2 ✓ sig.
Arginine and proline metabolism
ALDH18A1
 KEGG 1 / 50 120× 8.31e-3 5.07e-2
Ether lipid metabolism
SELENOI
 KEGG 1 / 50 120× 8.31e-3 5.07e-2
Biosynthesis of amino acids
ALDH18A1
 KEGG 1 / 75 80.1× 1.25e-2 6.50e-2
Glycerophospholipid metabolism
SELENOI
 KEGG 1 / 102 58.9× 1.69e-2 7.79e-2
Metabolic pathways
ALDH18A1, SELENOI
 KEGG 2 / 1,563 7.7× 1.69e-2 7.79e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
ornithine biosynthetic process
ALDH18A1
 GO:0006592 1 / 1 9,344× 1.07e-4 3.25e-3 ✓ sig.
citrulline biosynthetic process
ALDH18A1
 GO:0019240 1 / 4 2,336× 4.28e-4 8.53e-3 ✓ sig.
L-proline biosynthetic process
ALDH18A1
 GO:0055129 1 / 6 1,557× 6.42e-4 1.11e-2 ✓ sig.
glycerophospholipid biosynthetic process
SELENOI
 GO:0046474 1 / 7 1,335× 7.49e-4 1.23e-2 ✓ sig.
ether lipid biosynthetic process
SELENOI
 GO:0008611 1 / 8 1,168× 8.56e-4 1.33e-2 ✓ sig.
phosphatidylethanolamine biosynthetic process
SELENOI
 GO:0006646 1 / 12 779× 1.28e-3 1.67e-2 ✓ sig.
response to temperature stimulus
ALDH18A1
 GO:0009266 1 / 14 667× 1.50e-3 1.82e-2 ✓ sig.
glutamate metabolic process
ALDH18A1
 GO:0006536 1 / 15 623× 1.60e-3 1.88e-2 ✓ sig.
amino acid biosynthetic process
ALDH18A1
 GO:0008652 1 / 27 346× 2.89e-3 2.55e-2 ✓ sig.
phospholipid biosynthetic process
SELENOI
 GO:0008654 1 / 58 161× 6.20e-3 3.70e-2 ✓ sig.
myelination
SELENOI
 GO:0042552 1 / 73 128× 7.80e-3 4.13e-2 ✓ sig.
lipid metabolic process
SELENOI
 GO:0006629 1 / 840 11.1× 8.79e-2 1.52e-1

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cutis laxa, corneal clouding, and mental retardation P5CS deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a Spastic paraplegia 9b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, corneal clouding, and mental retardation Spastic paraplegia 9b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities Spastic paraplegia 9b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
P5CS deficiency Spastic paraplegia 9b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
De barsy syndrome Spastic paraplegia 9b, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a Spastic paraplegia 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, corneal clouding, and mental retardation Spastic paraplegia 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities Spastic paraplegia 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
P5CS deficiency Spastic paraplegia 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
De barsy syndrome Spastic paraplegia 9 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities P5CS deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
De barsy syndrome Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 0.500 1 6.46e-5 1.98e-4 ✓ sig.
De barsy syndrome P5CS deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, corneal clouding, and mental retardation Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, corneal clouding, and mental retardation De barsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a Cutis laxa, corneal clouding, and mental retardation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a P5CS deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal recessive, 3a De barsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant 3 Cutis laxa, autosomal recessive, 3a 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant 3 Cutis laxa, corneal clouding, and mental retardation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant 3 Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant 3 P5CS deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutis laxa, autosomal dominant 3 De barsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Complex spastic paraplegia De barsy syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Complex spastic paraplegia Spastic paraplegia 81, autosomal recessive 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Complex spastic paraplegia Cutis laxa, autosomal recessive, 3a 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Complex spastic paraplegia Cutis laxa, corneal clouding, and mental retardation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Complex spastic paraplegia Developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalities 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Complex spastic paraplegia P5CS deficiency 0.333 1 1.29e-4 3.27e-4 ✓ sig.