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 97
13
Diseases
40
Unique genes
0.222
Avg. similarity score
Synpolydactyly
Most-connected disease (7 links)
Disease
Searched: Neurocardiofaciodigital syndrome
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Neurocardiofaciodigital syndrome
Synpolydactyly
Brachydactyly-syndactyly syndrome
Brachymesophalangy
Penile hypospadia
Zygodactyly
Hemimelia of limb
Bone remodeling disease
Cryptorchidism
Osteochondrodysplasia, brachydactyly, and overlapping malformed digits
Biotinidase deficiency
Ghosal hematodiaphyseal dysplasia
Synpolydactyly, 3/3-prime/4, associated with metacarpal and metatarsal synostoses
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Synpolydactyly | 7 | 7 | 4 |
| Brachydactyly-syndactyly syndrome | 5 | 5 | 1 |
| Brachymesophalangy | 5 | 5 | 1 |
| Penile hypospadia | 5 | 5 | 8 |
| Zygodactyly | 5 | 5 | 1 |
| Hemimelia of limb | 3 | 3 | 2 |
| Bone remodeling disease | 2 | 2 | 12 |
| Cryptorchidism | 2 | 2 | 20 |
| Osteochondrodysplasia, brachydactyly, and overlapping malformed digits | 2 | 2 | 1 |
| Biotinidase deficiency | 1 | 1 | 1 |
| Ghosal hematodiaphyseal dysplasia | 1 | 1 | 1 |
| Neurocardiofaciodigital syndrome | 1 | 1 | 1 |
| Synpolydactyly, 3/3-prime/4, associated with metacarpal and metatarsal synostoses | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HOXD13 | 7 / 13 | Brachydactyly-syndactyly syndrome, Brachymesophalangy, Cryptorchidism, Hemimelia of limb and 3 more |
| CHST11 | 3 / 13 | Bone remodeling disease, Osteochondrodysplasia, brachydactyly, and overlapping malformed digits, Synpolydactyly |
| BTD | 2 / 13 | Biotinidase deficiency, Cryptorchidism |
| FBLN1 | 2 / 13 | Synpolydactyly, Synpolydactyly, 3/3-prime/4, associated with metacarpal and metatarsal synostoses |
| LSM1 | 2 / 13 | Cryptorchidism, Penile hypospadia |
| MAPKAPK5 | 2 / 13 | Neurocardiofaciodigital syndrome, Synpolydactyly |
| NIPBL | 2 / 13 | Cryptorchidism, Penile hypospadia |
| TBXAS1 | 2 / 13 | Ghosal hematodiaphyseal dysplasia, Penile hypospadia |
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 ⇵ |
|---|---|---|---|---|---|
| Relaxin receptors | Reactome | 2 / 8 | 75.1× | 2.99e-4 | 4.50e-3 ✓ sig. |
| Defective BTD causes biotidinase deficiency | Reactome | 1 / 1 | 300× | 3.33e-3 | 2.74e-2 ✓ sig. |
| Defective TBXAS1 causes Ghosal hematodiaphyseal dysplasia (GHDD) | Reactome | 1 / 1 | 300× | 3.33e-3 | 2.74e-2 ✓ sig. |
| Pathways of neurodegeneration - multiple diseases | KEGG | 6 / 480 | 3.8× | 4.77e-3 | 3.54e-2 ✓ sig. |
| Apoptosis - multiple species | KEGG | 2 / 32 | 18.8× | 5.04e-3 | 3.66e-2 ✓ sig. |
| Amyotrophic lateral sclerosis | KEGG | 5 / 368 | 4.1× | 7.16e-3 | 4.61e-2 ✓ sig. |
| Biotin metabolism | KEGG | 1 / 3 | 100× | 9.96e-3 | 5.67e-2 |
| The NLRP1 inflammasome | Reactome | 1 / 3 | 100× | 9.96e-3 | 5.67e-2 |
| Biosynthesis of aspirin-triggered D-series resolvins | Reactome | 1 / 3 | 100× | 9.96e-3 | 5.67e-2 |
| RUNX2 regulates osteoblast differentiation | Reactome | 1 / 3 | 100× | 9.96e-3 | 5.67e-2 |
| Apoptosis | KEGG | 3 / 137 | 6.6× | 1.05e-2 | 5.88e-2 |
| COPI-independent Golgi-to-ER retrograde traffic | Reactome | 2 / 51 | 11.8× | 1.24e-2 | 6.50e-2 |
| Caspase activation via Dependence Receptors in the absence of ligand | Reactome | 1 / 4 | 75.1× | 1.33e-2 | 6.74e-2 |
| Biosynthesis of D-series resolvins | Reactome | 1 / 4 | 75.1× | 1.33e-2 | 6.74e-2 |
| Biosynthesis of E-series 18(R)-resolvins | Reactome | 1 / 4 | 75.1× | 1.33e-2 | 6.74e-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 ⇵ |
|---|---|---|---|---|---|
| face morphogenesis | GO:0060325 | 4 / 33 | 56.6× | 7.04e-7 | 6.46e-5 ✓ sig. |
| regulation of developmental growth | GO:0048638 | 2 / 2 | 467× | 4.47e-6 | 2.89e-4 ✓ sig. |
| male gonad development | GO:0008584 | 5 / 117 | 20.0× | 4.88e-6 | 3.11e-4 ✓ sig. |
| morphogenesis of an epithelial fold | GO:0060571 | 2 / 4 | 234× | 2.67e-5 | 1.15e-3 ✓ sig. |
| response to testosterone | GO:0033574 | 3 / 36 | 38.9× | 6.18e-5 | 2.17e-3 ✓ sig. |
| regulation of intracellular signal transduction | GO:1902531 | 3 / 40 | 35.0× | 8.50e-5 | 2.74e-3 ✓ sig. |
| embryonic organ morphogenesis | GO:0048562 | 2 / 7 | 133× | 9.32e-5 | 2.93e-3 ✓ sig. |
| embryonic viscerocranium morphogenesis | GO:0048703 | 2 / 10 | 93.4× | 1.99e-4 | 5.06e-3 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 3 / 57 | 24.6× | 2.45e-4 | 5.87e-3 ✓ sig. |
| epithelial cell proliferation | GO:0050673 | 3 / 71 | 19.7× | 4.69e-4 | 9.13e-3 ✓ sig. |
| hippocampus development | GO:0021766 | 3 / 74 | 18.9× | 5.30e-4 | 9.88e-3 ✓ sig. |
| startle response | GO:0001964 | 2 / 18 | 51.9× | 6.69e-4 | 1.15e-2 ✓ sig. |
| seminiferous tubule development | GO:0072520 | 2 / 21 | 44.5× | 9.14e-4 | 1.39e-2 ✓ sig. |
| neuron apoptotic process | GO:0051402 | 3 / 98 | 14.3× | 1.20e-3 | 1.61e-2 ✓ sig. |
| response to tumor necrosis factor | GO:0034612 | 2 / 29 | 32.2× | 1.75e-3 | 1.99e-2 ✓ sig. |