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 156
10
Diseases
40
Unique genes
0.241
Avg. similarity score
Familial focal epilepsy with variable foci
Most-connected disease (6 links)
Disease
Searched: Short stature with non-specific skeletal abnormalities
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Short stature with non-specific skeletal abnormalities
Familial focal epilepsy with variable foci
Acromesomelic dysplasia
Epiphyseal chondrodysplasia, miura type
Short stature with non-specific skeletal abnormalities 1
Trident hand
Progressive myoclonic epilepsy
Focal epilepsy
Premature ovarian insufficiency
Progressive myoclonic epilepsy with renal failure
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Familial focal epilepsy with variable foci | 6 | 6 | 8 |
| Acromesomelic dysplasia | 5 | 5 | 7 |
| Epiphyseal chondrodysplasia, miura type | 5 | 5 | 1 |
| Short stature with non-specific skeletal abnormalities | 5 | 5 | 1 |
| Short stature with non-specific skeletal abnormalities 1 | 5 | 5 | 1 |
| Trident hand | 5 | 5 | 1 |
| Progressive myoclonic epilepsy | 3 | 3 | 25 |
| Focal epilepsy | 2 | 2 | 4 |
| Premature ovarian insufficiency | 1 | 1 | 4 |
| Progressive myoclonic epilepsy with renal failure | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NPR2 | 6 / 10 | Acromesomelic dysplasia, Epiphyseal chondrodysplasia, miura type, Familial focal epilepsy with variable foci, Short stature with non-specific skeletal abnormalities and 2 more |
| DEPDC5 | 3 / 10 | Familial focal epilepsy with variable foci, Focal epilepsy, Progressive myoclonic epilepsy |
| NPRL2 | 3 / 10 | Familial focal epilepsy with variable foci, Focal epilepsy, Progressive myoclonic epilepsy |
| NPRL3 | 3 / 10 | Familial focal epilepsy with variable foci, Focal epilepsy, Progressive myoclonic epilepsy |
| BMPR1B | 2 / 10 | Acromesomelic dysplasia, Premature ovarian insufficiency |
| SEMA6B | 2 / 10 | Progressive myoclonic epilepsy, Progressive myoclonic epilepsy with renal failure |
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 ⇵ |
|---|---|---|---|---|---|
| Molecules associated with elastic fibres | Reactome | 3 / 38 | 23.7× | 2.66e-4 | 4.11e-3 ✓ sig. |
| Myoclonic epilepsy of Lafora | Reactome | 2 / 9 | 66.7× | 3.84e-4 | 5.44e-3 ✓ sig. |
| Amino acids regulate mTORC1 | Reactome | 3 / 55 | 16.4× | 7.96e-4 | 9.52e-3 ✓ sig. |
| Glycogen synthesis | Reactome | 2 / 16 | 37.5× | 1.26e-3 | 1.35e-2 ✓ sig. |
| TGF-beta signaling pathway | KEGG | 3 / 108 | 8.3× | 5.49e-3 | 3.87e-2 ✓ sig. |
| Defective DHDDS causes retinitis pigmentosa 59 | Reactome | 1 / 2 | 150× | 6.65e-3 | 4.39e-2 ✓ sig. |
| mTOR signaling pathway | KEGG | 3 / 158 | 5.7× | 1.55e-2 | 7.39e-2 |
| STING mediated induction of host immune responses | Reactome | 1 / 5 | 60.1× | 1.65e-2 | 7.67e-2 |
| Synthesis of Dolichyl-phosphate | Reactome | 1 / 6 | 50.0× | 1.98e-2 | 8.52e-2 |
| Stimuli-sensing channels | Reactome | 2 / 79 | 7.6× | 2.84e-2 | 1.05e-1 |
| Hormone signaling | KEGG | 3 / 219 | 4.1× | 3.60e-2 | 1.20e-1 |
| cGMP effects | Reactome | 1 / 11 | 27.3× | 3.60e-2 | 1.20e-1 |
| Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation | Reactome | 1 / 11 | 27.3× | 3.60e-2 | 1.20e-1 |
| Physiological factors | Reactome | 1 / 12 | 25.0× | 3.93e-2 | 1.26e-1 |
| IRF3-mediated induction of type I IFN | Reactome | 1 / 13 | 23.1× | 4.25e-2 | 1.32e-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 ⇵ |
|---|---|---|---|---|---|
| chondrocyte differentiation | GO:0002062 | 4 / 61 | 30.6× | 8.60e-6 | 4.84e-4 ✓ sig. |
| positive regulation of chondrocyte differentiation | GO:0032332 | 3 / 20 | 70.1× | 1.01e-5 | 5.49e-4 ✓ sig. |
| regulation of protein localization to plasma membrane | GO:1903076 | 3 / 27 | 51.9× | 2.56e-5 | 1.11e-3 ✓ sig. |
| regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | GO:0090092 | 2 / 6 | 156× | 6.67e-5 | 2.28e-3 ✓ sig. |
| action potential | GO:0001508 | 3 / 53 | 26.4× | 1.98e-4 | 5.04e-3 ✓ sig. |
| response to fibroblast growth factor | GO:0071774 | 2 / 11 | 84.9× | 2.43e-4 | 5.82e-3 ✓ sig. |
| cellular response to amino acid starvation | GO:0034198 | 3 / 60 | 23.4× | 2.86e-4 | 6.55e-3 ✓ sig. |
| negative regulation of TORC1 signaling | GO:1904262 | 3 / 71 | 19.7× | 4.69e-4 | 9.13e-3 ✓ sig. |
| glycogen biosynthetic process | GO:0005978 | 2 / 18 | 51.9× | 6.69e-4 | 1.15e-2 ✓ sig. |
| BMP signaling pathway | GO:0030509 | 3 / 88 | 15.9× | 8.79e-4 | 1.36e-2 ✓ sig. |
| cartilage development | GO:0051216 | 3 / 89 | 15.7× | 9.08e-4 | 1.39e-2 ✓ sig. |
| post-anal tail morphogenesis | GO:0036342 | 2 / 21 | 44.5× | 9.14e-4 | 1.39e-2 ✓ sig. |
| regulation of protein ubiquitination | GO:0031396 | 2 / 21 | 44.5× | 9.14e-4 | 1.39e-2 ✓ sig. |
| positive regulation of autophagy | GO:0010508 | 3 / 92 | 15.2× | 1.00e-3 | 1.46e-2 ✓ sig. |
| negative regulation of chondrocyte differentiation | GO:0032331 | 2 / 23 | 40.6× | 1.10e-3 | 1.54e-2 ✓ sig. |