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.

← Back to all clusters

Cluster 308

6 diseases · 8 shared-gene connections
6 Diseases
27 Unique genes
0.157 Avg. similarity score
Epiphyseal dysplasia Most-connected disease (5 links)
Log in to save this analysis

Save This Analysis

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 ⇵
Epiphyseal dysplasia 5 5 10
Marshall syndrome 3 3 19
Stickler syndrome 3 3 14
Stickler syndrome, type 4 3 3 1
Comp-related skeletal dysplasia 1 1 1
Laryngeal hypoplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL9A1 4 / 6 Epiphyseal dysplasia, Marshall syndrome, Stickler syndrome, Stickler syndrome, type 4
COL2A1 3 / 6 Epiphyseal dysplasia, Marshall syndrome, Stickler syndrome
COL9A2 3 / 6 Epiphyseal dysplasia, Marshall syndrome, Stickler syndrome
COL9A3 3 / 6 Epiphyseal dysplasia, Marshall syndrome, Stickler syndrome
BMP4 2 / 6 Marshall syndrome, Stickler syndrome
COL11A1 2 / 6 Marshall syndrome, Stickler syndrome
COL11A2 2 / 6 Marshall syndrome, Stickler syndrome
COL1A1 2 / 6 Epiphyseal dysplasia, Stickler syndrome
COMP 2 / 6 Comp-related skeletal dysplasia, Epiphyseal dysplasia
FOXP4 2 / 6 Epiphyseal dysplasia, Laryngeal hypoplasia
LOXL3 2 / 6 Marshall syndrome, Stickler syndrome
LRP2 2 / 6 Marshall syndrome, Stickler syndrome
SLC26A2 2 / 6 Epiphyseal dysplasia, Marshall syndrome
VCAN 2 / 6 Marshall syndrome, Stickler syndrome
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 ⇵
Collagen biosynthesis and modifying enzymes
COL11A1, COL9A1, COL9A2, COL9A3, COL1A1, COL2A1, COL11A2, P3H2, PLOD3, COL4A3
 Reactome 10 / 67 66.4× 1.13e-16 5.07e-14 ✓ sig.
Collagen chain trimerization
COL11A1, COL9A1, COL9A2, COL9A3, COL1A1, COL2A1, COL11A2, COL4A3
 Reactome 8 / 44 80.9× 3.49e-14 9.71e-12 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL11A1, COL9A1, COL9A2, COL9A3, COL1A1, COL2A1, COL11A2, COL4A3
 Reactome 8 / 51 69.8× 1.24e-13 3.10e-11 ✓ sig.
ECM proteoglycans
COL9A1, COL9A2, COL9A3, COMP, COL1A1, MATN3, COL2A1, VCAN
 Reactome 8 / 51 69.8× 1.24e-13 3.10e-11 ✓ sig.
Protein digestion and absorption
COL11A1, COL9A1, COL9A2, COL9A3, COL1A1, COL2A1, COL11A2, KCNJ13, COL4A3
 KEGG 9 / 103 38.9× 7.25e-13 1.62e-10 ✓ sig.
Integrin cell surface interactions
COL9A1, COL9A2, COL9A3, COMP, COL1A1, COL2A1, COL4A3
 Reactome 7 / 81 38.4× 3.88e-10 4.86e-8 ✓ sig.
ECM-receptor interaction
COL9A1, COL9A2, COL9A3, COMP, COL1A1, COL2A1, COL4A3
 KEGG 7 / 89 35.0× 7.60e-10 8.77e-8 ✓ sig.
NCAM1 interactions
COL9A1, COL9A2, COL9A3, COL2A1, COL4A3
 Reactome 5 / 21 106× 7.71e-10 8.86e-8 ✓ sig.
Cytoskeleton in muscle cells
COL11A1, COL9A1, COL9A2, COL9A3, COMP, COL1A1, COL11A2, VCAN, COL4A3
 KEGG 9 / 232 17.3× 1.11e-9 1.24e-7 ✓ sig.
Non-integrin membrane-ECM interactions
COL11A1, COL1A1, COL2A1, COL11A2, COL4A3
 Reactome 5 / 24 92.7× 1.60e-9 1.69e-7 ✓ sig.
Signaling by PDGF
COL9A1, COL9A2, COL9A3, COL2A1, COL4A3
 Reactome 5 / 33 67.4× 8.82e-9 7.84e-7 ✓ sig.
Collagen degradation
COL11A1, COL1A1, COL2A1, COL11A2, COL4A3
 Reactome 5 / 52 42.8× 9.39e-8 6.20e-6 ✓ sig.
Focal adhesion
COL9A1, COL9A2, COL9A3, COMP, COL1A1, COL2A1, COL4A3
 KEGG 7 / 203 15.3× 2.37e-7 1.39e-5 ✓ sig.
MET activates PTK2 signaling
COL11A1, COL1A1, COL2A1, COL11A2
 Reactome 4 / 30 59.3× 5.33e-7 2.83e-5 ✓ sig.
Extracellular matrix organization
COL1A1, COL2A1, COL4A3
 Reactome 3 / 15 89.0× 4.53e-6 1.75e-4 ✓ 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 ⇵
collagen fibril organization
COL11A1, LOXL3, COMP, COL1A1, COL2A1, COL11A2, PLOD3
 GO:0030199 7 / 65 74.5× 3.71e-12 1.49e-9 ✓ sig.
skeletal system development
COL9A2, COMP, COL1A1, MATN3, COL2A1, BMP4, COL11A2, VCAN
 GO:0001501 8 / 151 36.7× 2.94e-11 9.57e-9 ✓ sig.
sensory perception of sound
COL11A1, COL1A1, COL2A1, COL11A2, LRP2, SLITRK6, CDH23, COL4A3
 GO:0007605 8 / 162 34.2× 5.17e-11 1.59e-8 ✓ sig.
cartilage development
COL11A1, COMP, MATN3, COL2A1, BMP4, COL11A2
 GO:0051216 6 / 89 46.7× 2.69e-9 5.36e-7 ✓ sig.
inner ear morphogenesis
COL11A1, COL2A1, SLITRK6, CDH23
 GO:0042472 4 / 65 42.6× 2.20e-6 1.56e-4 ✓ sig.
endochondral ossification
COL1A1, COL2A1, BMP4
 GO:0001958 3 / 31 67.0× 1.18e-5 5.92e-4 ✓ sig.
tendon development
COL11A1, COMP
 GO:0035989 2 / 4 346× 1.20e-5 6.02e-4 ✓ sig.
visual perception
COL11A1, COL1A1, COL2A1, SLITRK6, CDH23
 GO:0007601 5 / 215 16.1× 1.26e-5 6.27e-4 ✓ sig.
ossification
COMP, COL1A1, COL2A1, BMP4
 GO:0001503 4 / 110 25.2× 1.80e-5 8.24e-4 ✓ sig.
skeletal system morphogenesis
COL11A1, COL1A1, COL2A1
 GO:0048705 3 / 45 46.1× 3.67e-5 1.43e-3 ✓ sig.
cartilage development involved in endochondral bone morphogenesis
COL1A1, COL2A1
 GO:0060351 2 / 9 154× 7.19e-5 2.36e-3 ✓ sig.
heart morphogenesis
COL11A1, COL2A1, BMP4
 GO:0003007 3 / 61 34.0× 9.15e-5 2.83e-3 ✓ sig.
chondrocyte differentiation
SLC26A2, COL2A1, BMP4
 GO:0002062 3 / 61 34.0× 9.15e-5 2.83e-3 ✓ sig.
proteoglycan metabolic process
COL11A1, COL2A1
 GO:0006029 2 / 11 126× 1.10e-4 3.23e-3 ✓ sig.
embryonic skeletal joint morphogenesis
COL2A1, BMP4
 GO:0060272 2 / 11 126× 1.10e-4 3.23e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Marshall syndrome Stickler syndrome 0.417 10 4.48e-28 1.35e-26 ✓ sig.
Epiphyseal dysplasia Stickler syndrome 0.250 5 6.98e-14 9.66e-13 ✓ sig.
Epiphyseal dysplasia Marshall syndrome 0.200 5 4.05e-13 5.37e-12 ✓ sig.
Comp-related skeletal dysplasia Epiphyseal dysplasia 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Epiphyseal dysplasia Laryngeal hypoplasia 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Epiphyseal dysplasia Stickler syndrome, type 4 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Stickler syndrome Stickler syndrome, type 4 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Marshall syndrome Stickler syndrome, type 4 0.050 1 1.23e-3 1.97e-3 ✓ sig.