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 467

6 diseases · 11 shared-gene connections
6 Diseases
4 Unique genes
0.326 Avg. similarity score
Combined osteogenesis imperfecta and ehlers-danlos syndrome Most-connected disease (5 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 ⇵
Combined osteogenesis imperfecta and ehlers-danlos syndrome 5 5 2
Caffey disease 4 4 1
Cortical congenital hyperostosis 4 4 2
Maternal hypertension 4 4 1
Rhizomelia 4 4 2
Ehlers-danlos syndrome, cardiac valvular type 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL1A1 5 / 6 Caffey disease, Combined osteogenesis imperfecta and ehlers-danlos syndrome , Cortical congenital hyperostosis, Maternal hypertension and 1 more
COL1A2 2 / 6 Combined osteogenesis imperfecta and ehlers-danlos syndrome , Ehlers-danlos syndrome, cardiac valvular type
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 ⇵
Platelet Aggregation (Plug Formation)
COL1A1, COL1A2
 Reactome 2 / 8 751× 2.33e-6 8.57e-5 ✓ sig.
Platelet Adhesion to exposed collagen
COL1A1, COL1A2
 Reactome 2 / 11 546× 4.57e-6 1.53e-4 ✓ sig.
GP1b-IX-V activation signalling
COL1A1, COL1A2
 Reactome 2 / 12 500× 5.49e-6 1.77e-4 ✓ sig.
Extracellular matrix organization
COL1A1, COL1A2
 Reactome 2 / 15 400× 8.72e-6 2.60e-4 ✓ sig.
Anchoring fibril formation
COL1A1, COL1A2
 Reactome 2 / 15 400× 8.72e-6 2.60e-4 ✓ sig.
Crosslinking of collagen fibrils
COL1A1, COL1A2
 Reactome 2 / 18 334× 1.27e-5 3.55e-4 ✓ sig.
Non-integrin membrane-ECM interactions
COL1A1, COL1A2
 Reactome 2 / 24 250× 2.29e-5 5.83e-4 ✓ sig.
Cytoskeleton in muscle cells
COL1A1, COL1A2, LBR
 KEGG 3 / 232 38.8× 2.81e-5 6.86e-4 ✓ sig.
MET activates PTK2 signaling
COL1A1, COL1A2
 Reactome 2 / 30 200× 3.61e-5 8.42e-4 ✓ sig.
GPVI-mediated activation cascade
COL1A1, COL1A2
 Reactome 2 / 34 177× 4.65e-5 1.03e-3 ✓ sig.
Collagen chain trimerization
COL1A1, COL1A2
 Reactome 2 / 44 136× 7.83e-5 1.56e-3 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL1A1, COL1A2
 Reactome 2 / 51 118× 1.06e-4 1.98e-3 ✓ sig.
ECM proteoglycans
COL1A1, COL1A2
 Reactome 2 / 51 118× 1.06e-4 1.98e-3 ✓ sig.
Collagen degradation
COL1A1, COL1A2
 Reactome 2 / 52 115× 1.10e-4 2.04e-3 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL1A1, COL1A2
 Reactome 2 / 67 89.6× 1.83e-4 3.06e-3 ✓ 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 ⇵
skin morphogenesis
COL1A1, COL1A2
 GO:0043589 2 / 13 719× 2.68e-6 1.92e-4 ✓ sig.
cellular response to amino acid stimulus
COL1A1, COL1A2
 GO:0071230 2 / 64 146× 6.90e-5 2.34e-3 ✓ sig.
collagen fibril organization
COL1A1, COL1A2
 GO:0030199 2 / 65 144× 7.12e-5 2.40e-3 ✓ sig.
blood vessel development
COL1A1, COL1A2
 GO:0001568 2 / 70 133× 8.26e-5 2.69e-3 ✓ sig.
animal organ development
COL1A1, COL1A2
 GO:0048513 2 / 102 91.6× 1.76e-4 4.63e-3 ✓ sig.
globoside biosynthetic process
A4GALT
 GO:0001576 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
cellular response to vitamin E
COL1A1
 GO:0071306 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
protein heterotrimerization
COL1A2
 GO:0070208 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
skeletal system development
COL1A1, COL1A2
 GO:0001501 2 / 151 61.9× 3.85e-4 7.96e-3 ✓ sig.
cellular response to fluoride
COL1A1
 GO:1902618 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
tooth mineralization
COL1A1
 GO:0034505 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
response to fluoride
COL1A1
 GO:1902617 1 / 4 1,168× 8.56e-4 1.33e-2 ✓ sig.
intramembranous ossification
COL1A1
 GO:0001957 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
bone trabecula formation
COL1A1
 GO:0060346 1 / 8 584× 1.71e-3 1.96e-2 ✓ sig.
neutrophil differentiation
LBR
 GO:0030223 1 / 8 584× 1.71e-3 1.96e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Caffey disease Maternal hypertension 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Caffey disease Combined osteogenesis imperfecta and ehlers-danlos syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Caffey disease Cortical congenital hyperostosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Caffey disease Rhizomelia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Maternal hypertension 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Ehlers-danlos syndrome, cardiac valvular type 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cortical congenital hyperostosis Maternal hypertension 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Maternal hypertension Rhizomelia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Cortical congenital hyperostosis 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Rhizomelia 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Cortical congenital hyperostosis Rhizomelia 0.250 1 2.58e-4 5.38e-4 ✓ sig.