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 211
8
Diseases
38
Unique genes
0.053
Avg. similarity score
Spondyloepimetaphyseal dysplasia
Most-connected disease (6 links)
Disease
Searched: B3GALT6-congenital disorder of glycosylation
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B3GALT6-congenital disorder of glycosylation
Spondyloepimetaphyseal dysplasia
Spondyloepiphyseal dysplasia
Short stature spectrum
Hoxha-aliu syndrome
spondyloepimetaphyseal dysplasia with joint laxity, type 3
spondyloepimetaphyseal dysplasia, genevieve type
spondyloepiphyseal dysplasia, kondo-fu type
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Spondyloepimetaphyseal dysplasia | 6 | 6 | 25 |
| Spondyloepiphyseal dysplasia | 4 | 4 | 18 |
| B3GALT6-congenital disorder of glycosylation | 2 | 2 | 1 |
| Short stature spectrum | 2 | 2 | 1 |
| Hoxha-aliu syndrome | 1 | 1 | 1 |
| spondyloepimetaphyseal dysplasia with joint laxity, type 3 | 1 | 1 | 1 |
| spondyloepimetaphyseal dysplasia, genevieve type | 1 | 1 | 1 |
| spondyloepiphyseal dysplasia, kondo-fu type | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ACAN | 3 / 8 | Short stature spectrum, Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia |
| B3GALT6 | 3 / 8 | B3GALT6-congenital disorder of glycosylation, Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia |
| COL2A1 | 2 / 8 | Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia |
| ERI1 | 2 / 8 | Hoxha-aliu syndrome, Spondyloepimetaphyseal dysplasia |
| EXOC6B | 2 / 8 | Spondyloepimetaphyseal dysplasia, spondyloepimetaphyseal dysplasia with joint laxity, type 3 |
| MBTPS1 | 2 / 8 | Spondyloepiphyseal dysplasia, spondyloepiphyseal dysplasia, kondo-fu type |
| NANS | 2 / 8 | Spondyloepimetaphyseal dysplasia, spondyloepimetaphyseal dysplasia, genevieve type |
| RPL13 | 2 / 8 | Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia |
| TRPV4 | 2 / 8 | Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia |
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 ⇵ |
|---|---|---|---|---|---|
| ECM proteoglycans | Reactome | 5 / 51 | 31.0× | 5.10e-7 | 2.90e-5 ✓ sig. |
| Defective B3GALT6 causes EDSP2 and SEMDJL1 | Reactome | 3 / 20 | 47.4× | 3.21e-5 | 9.28e-4 ✓ sig. |
| Non-integrin membrane-ECM interactions | Reactome | 3 / 24 | 39.5× | 5.65e-5 | 1.47e-3 ✓ sig. |
| A tetrasaccharide linker sequence is required for GAG synthesis | Reactome | 3 / 26 | 36.5× | 7.23e-5 | 1.79e-3 ✓ sig. |
| Defective CHST3 causes SEDCJD | Reactome | 2 / 8 | 79.0× | 2.70e-4 | 5.08e-3 ✓ sig. |
| Keratan sulfate degradation | Reactome | 2 / 13 | 48.6× | 7.44e-4 | 1.12e-2 ✓ sig. |
| Degradation of the extracellular matrix | Reactome | 3 / 70 | 13.5× | 1.38e-3 | 1.80e-2 ✓ sig. |
| Defective B4GALT7 causes EDS, progeroid type | Reactome | 2 / 20 | 31.6× | 1.79e-3 | 2.18e-2 ✓ sig. |
| Defective B3GAT3 causes JDSSDHD | Reactome | 2 / 20 | 31.6× | 1.79e-3 | 2.18e-2 ✓ sig. |
| Chondroitin sulfate biosynthesis | Reactome | 2 / 20 | 31.6× | 1.79e-3 | 2.18e-2 ✓ sig. |
| Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | KEGG | 2 / 21 | 30.1× | 1.97e-3 | 2.34e-2 ✓ sig. |
| HS-GAG degradation | Reactome | 2 / 22 | 28.7× | 2.16e-3 | 2.51e-2 ✓ sig. |
| Defective ABCD1 causes adrenoleukodystrophy (ALD) | Reactome | 1 / 1 | 316× | 3.16e-3 | 3.27e-2 ✓ sig. |
| MPS IV - Morquio syndrome B | Reactome | 1 / 1 | 316× | 3.16e-3 | 3.27e-2 ✓ sig. |
| Defective PAPSS2 causes SEMD-PA | Reactome | 1 / 1 | 316× | 3.16e-3 | 3.27e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| cartilage condensation | GO:0001502 | 3 / 21 | 70.3× | 1.01e-5 | 5.42e-4 ✓ sig. |
| cartilage development | GO:0051216 | 4 / 89 | 22.1× | 3.14e-5 | 1.30e-3 ✓ sig. |
| ossification | GO:0001503 | 4 / 110 | 17.9× | 7.19e-5 | 2.45e-3 ✓ sig. |
| connective tissue development | GO:0061448 | 2 / 7 | 141× | 8.40e-5 | 2.76e-3 ✓ sig. |
| cartilage development involved in endochondral bone morphogenesis | GO:0060351 | 2 / 9 | 109× | 1.44e-4 | 4.09e-3 ✓ sig. |
| regulation of intracellular estrogen receptor signaling pathway | GO:0033146 | 2 / 10 | 98.4× | 1.79e-4 | 4.83e-3 ✓ sig. |
| positive regulation of extracellular matrix disassembly | GO:0090091 | 2 / 11 | 89.4× | 2.19e-4 | 5.54e-3 ✓ sig. |
| skeletal system development | GO:0001501 | 4 / 151 | 13.0× | 2.44e-4 | 6.01e-3 ✓ sig. |
| chondrocyte proliferation | GO:0035988 | 2 / 15 | 65.6× | 4.16e-4 | 8.73e-3 ✓ sig. |
| bone development | GO:0060348 | 3 / 76 | 19.4× | 4.92e-4 | 9.77e-3 ✓ sig. |
| ribosome disassembly | GO:0032790 | 2 / 22 | 44.7× | 9.07e-4 | 1.47e-2 ✓ sig. |
| regulation of bone mineralization | GO:0030500 | 2 / 24 | 41.0× | 1.08e-3 | 1.64e-2 ✓ sig. |
| chondroitin sulfate proteoglycan biosynthetic process | GO:0050650 | 2 / 26 | 37.8× | 1.27e-3 | 1.80e-2 ✓ sig. |
| tissue homeostasis | GO:0001894 | 2 / 27 | 36.4× | 1.37e-3 | 1.88e-2 ✓ sig. |
| endochondral ossification | GO:0001958 | 2 / 31 | 31.7× | 1.80e-3 | 2.21e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Spondyloepimetaphyseal dysplasia | Spondyloepiphyseal dysplasia | 0.128 | 5 | 6.23e-11 | 6.32e-10 ✓ sig. |
| B3GALT6-congenital disorder of glycosylation | Spondyloepiphyseal dysplasia | 0.053 | 1 | 1.17e-3 | 1.90e-3 ✓ sig. |
| Short stature spectrum | Spondyloepiphyseal dysplasia | 0.053 | 1 | 1.17e-3 | 1.90e-3 ✓ sig. |
| Spondyloepiphyseal dysplasia | spondyloepiphyseal dysplasia, kondo-fu type | 0.053 | 1 | 1.17e-3 | 1.90e-3 ✓ sig. |
| B3GALT6-congenital disorder of glycosylation | Spondyloepimetaphyseal dysplasia | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Hoxha-aliu syndrome | Spondyloepimetaphyseal dysplasia | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Short stature spectrum | Spondyloepimetaphyseal dysplasia | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Spondyloepimetaphyseal dysplasia | spondyloepimetaphyseal dysplasia with joint laxity, type 3 | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Spondyloepimetaphyseal dysplasia | spondyloepimetaphyseal dysplasia, genevieve type | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |