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 305
6
Diseases
18
Unique genes
0.109
Avg. similarity score
Chondrodysplasia
Most-connected disease (5 links)
Disease
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Chondrodysplasia
Rhizomelic chondrodysplasia punctata
alkylglycerone-phosphate synthase deficiency
glyceronephosphate O-acyltransferase deficiency
X-linked dominant chondrodysplasia chassaing-lacombe type
chondrodysplasia with joint dislocations, gpapp type
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Chondrodysplasia | 5 | 5 | 17 |
| Rhizomelic chondrodysplasia punctata | 3 | 3 | 5 |
| alkylglycerone-phosphate synthase deficiency | 2 | 2 | 1 |
| glyceronephosphate O-acyltransferase deficiency | 2 | 2 | 1 |
| X-linked dominant chondrodysplasia chassaing-lacombe type | 1 | 1 | 1 |
| chondrodysplasia with joint dislocations, gpapp type | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AGPS | 3 / 6 | alkylglycerone-phosphate synthase deficiency, Chondrodysplasia, Rhizomelic chondrodysplasia punctata |
| GNPAT | 3 / 6 | Chondrodysplasia, glyceronephosphate O-acyltransferase deficiency, Rhizomelic chondrodysplasia punctata |
| BPNT2 | 2 / 6 | Chondrodysplasia, chondrodysplasia with joint dislocations, gpapp type |
| HDAC6 | 2 / 6 | Chondrodysplasia, X-linked dominant chondrodysplasia chassaing-lacombe type |
| PEX5 | 2 / 6 | Chondrodysplasia, Rhizomelic chondrodysplasia punctata |
| PEX7 | 2 / 6 | Chondrodysplasia, Rhizomelic chondrodysplasia punctata |
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 ⇵ |
|---|---|---|---|---|---|
| Peroxisomal protein import | Reactome | 4 / 63 | 42.4× | 1.99e-6 | 8.76e-5 ✓ sig. |
| Peroxisome | KEGG | 4 / 83 | 32.2× | 6.03e-6 | 2.20e-4 ✓ sig. |
| Plasmalogen biosynthesis | Reactome | 2 / 3 | 445× | 6.36e-6 | 2.29e-4 ✓ sig. |
| Aggrephagy | Reactome | 2 / 40 | 33.4× | 1.60e-3 | 1.94e-2 ✓ sig. |
| Cholesterol biosynthesis via desmosterol | Reactome | 1 / 4 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| Cholesterol biosynthesis via lathosterol | Reactome | 1 / 4 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| TGF-beta signaling pathway | KEGG | 2 / 108 | 12.4× | 1.12e-2 | 7.34e-2 |
| Sulfur metabolism | KEGG | 1 / 10 | 66.7× | 1.49e-2 | 8.66e-2 |
| Pexophagy | Reactome | 1 / 10 | 66.7× | 1.49e-2 | 8.66e-2 |
| HSF1 activation | Reactome | 1 / 12 | 55.6× | 1.78e-2 | 9.67e-2 |
| Transcriptional regulation by RUNX2 | Reactome | 1 / 12 | 55.6× | 1.78e-2 | 9.67e-2 |
| The activation of arylsulfatases | Reactome | 1 / 13 | 51.3× | 1.93e-2 | 1.01e-1 |
| Hippo signaling pathway | KEGG | 2 / 157 | 8.5× | 2.27e-2 | 1.10e-1 |
| Cytosolic sulfonation of small molecules | Reactome | 1 / 18 | 37.1× | 2.67e-2 | 1.21e-1 |
| Class B/2 (Secretin family receptors) | Reactome | 1 / 18 | 37.1× | 2.67e-2 | 1.21e-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 ⇵ |
|---|---|---|---|---|---|
| ether lipid biosynthetic process | GO:0008611 | 3 / 8 | 389× | 4.19e-8 | 5.83e-6 ✓ sig. |
| chondrocyte development | GO:0002063 | 3 / 21 | 148× | 9.87e-7 | 8.21e-5 ✓ sig. |
| skeletal system development | GO:0001501 | 4 / 151 | 27.5× | 1.15e-5 | 5.80e-4 ✓ sig. |
| chondroitin sulfate proteoglycan metabolic process | GO:0050654 | 2 / 6 | 346× | 1.31e-5 | 6.45e-4 ✓ sig. |
| chondrocyte differentiation | GO:0002062 | 3 / 61 | 51.1× | 2.61e-5 | 1.10e-3 ✓ sig. |
| protein targeting to peroxisome | GO:0006625 | 2 / 10 | 208× | 3.93e-5 | 1.50e-3 ✓ sig. |
| protein import into peroxisome matrix | GO:0016558 | 2 / 14 | 148× | 7.92e-5 | 2.54e-3 ✓ sig. |
| cartilage development | GO:0051216 | 3 / 89 | 35.0× | 8.09e-5 | 2.59e-3 ✓ sig. |
| positive regulation of chondrocyte differentiation | GO:0032332 | 2 / 20 | 104× | 1.65e-4 | 4.39e-3 ✓ sig. |
| proteoglycan biosynthetic process | GO:0030166 | 2 / 21 | 98.9× | 1.82e-4 | 4.74e-3 ✓ sig. |
| peroxisome organization | GO:0007031 | 2 / 23 | 90.3× | 2.19e-4 | 5.37e-3 ✓ sig. |
| endochondral ossification | GO:0001958 | 2 / 31 | 67.0× | 4.01e-4 | 8.22e-3 ✓ sig. |
| cell surface receptor protein serine/threonine kinase signaling pathway | GO:0007178 | 2 / 33 | 62.9× | 4.55e-4 | 8.97e-3 ✓ sig. |
| negative regulation of protein-containing complex assembly | GO:0031333 | 2 / 36 | 57.7× | 5.41e-4 | 1.01e-2 ✓ sig. |
| fatty acid beta-oxidation | GO:0006635 | 2 / 48 | 43.3× | 9.63e-4 | 1.47e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Chondrodysplasia | Rhizomelic chondrodysplasia punctata | 0.211 | 4 | 5.08e-12 | 6.06e-11 ✓ sig. |
| alkylglycerone-phosphate synthase deficiency | Rhizomelic chondrodysplasia punctata | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| glyceronephosphate O-acyltransferase deficiency | Rhizomelic chondrodysplasia punctata | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| alkylglycerone-phosphate synthase deficiency | Chondrodysplasia | 0.056 | 1 | 1.10e-3 | 1.81e-3 ✓ sig. |
| Chondrodysplasia | chondrodysplasia with joint dislocations, gpapp type | 0.056 | 1 | 1.10e-3 | 1.81e-3 ✓ sig. |
| Chondrodysplasia | glyceronephosphate O-acyltransferase deficiency | 0.056 | 1 | 1.10e-3 | 1.81e-3 ✓ sig. |
| Chondrodysplasia | X-linked dominant chondrodysplasia chassaing-lacombe type | 0.056 | 1 | 1.10e-3 | 1.81e-3 ✓ sig. |