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 468
6
Diseases
5
Unique genes
0.281
Avg. similarity score
Congenital palmoplantar and perioral keratoderma of olmsted
Most-connected disease (4 links)
Disease
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Congenital palmoplantar and perioral keratoderma of olmsted
Olmsted syndrome
Palmoplantar keratoderma, nonepidermolytic, focal
Palmoplantar keratoderma, nonepidermolytic, focal 2
Erythrokeratodermia variabilis et progressiva 7
Palmoplantar keratoderma, nonepidermolytic, focal, 1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital palmoplantar and perioral keratoderma of olmsted | 4 | 4 | 3 |
| Olmsted syndrome | 4 | 4 | 4 |
| Palmoplantar keratoderma, nonepidermolytic, focal | 4 | 4 | 2 |
| Palmoplantar keratoderma, nonepidermolytic, focal 2 | 3 | 3 | 1 |
| Erythrokeratodermia variabilis et progressiva 7 | 2 | 2 | 1 |
| Palmoplantar keratoderma, nonepidermolytic, focal, 1 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TRPV3 | 4 / 6 | Congenital palmoplantar and perioral keratoderma of olmsted, Olmsted syndrome, Palmoplantar keratoderma, nonepidermolytic, focal, Palmoplantar keratoderma, nonepidermolytic, focal 2 |
| PERP | 3 / 6 | Congenital palmoplantar and perioral keratoderma of olmsted, Erythrokeratodermia variabilis et progressiva 7, Olmsted syndrome |
| KRT16 | 2 / 6 | Palmoplantar keratoderma, nonepidermolytic, focal, Palmoplantar keratoderma, nonepidermolytic, focal, 1 |
| MBTPS2 | 2 / 6 | Congenital palmoplantar and perioral keratoderma of olmsted, Olmsted 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 ⇵ |
|---|---|---|---|---|---|
| Formation of the cornified envelope | Reactome | 2 / 130 | 37.0× | 1.14e-3 | 1.25e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperones | Reactome | 1 / 4 | 601× | 1.66e-3 | 1.66e-2 ✓ sig. |
| CREB3 factors activate genes | Reactome | 1 / 5 | 480× | 2.08e-3 | 1.96e-2 ✓ sig. |
| Regulation of cholesterol biosynthesis by SREBP (SREBF) | Reactome | 1 / 7 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain | Reactome | 1 / 14 | 172× | 5.82e-3 | 4.03e-2 ✓ sig. |
| TRP channels | Reactome | 1 / 28 | 85.8× | 1.16e-2 | 6.22e-2 |
| p53 signaling pathway | KEGG | 1 / 75 | 32.0× | 3.08e-2 | 1.10e-1 |
| Inflammatory mediator regulation of TRP channels | KEGG | 1 / 99 | 24.3× | 4.05e-2 | 1.28e-1 |
| Staphylococcus aureus infection | KEGG | 1 / 99 | 24.3× | 4.05e-2 | 1.28e-1 |
| Estrogen signaling pathway | KEGG | 1 / 139 | 17.3× | 5.66e-2 | 1.55e-1 |
| Keratinization | Reactome | 1 / 152 | 15.8× | 6.17e-2 | 1.63e-1 |
| Protein processing in endoplasmic reticulum | KEGG | 1 / 171 | 14.0× | 6.92e-2 | 1.74e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of hair cycle | GO:0042636 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| spermatocyte division | GO:0048137 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| bone maturation | GO:0070977 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| meiotic DNA repair synthesis | GO:0000711 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| regulation of response to endoplasmic reticulum stress | GO:1905897 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| keratinocyte migration | GO:0051546 | 1 / 6 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| reproductive system development | GO:0061458 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| ATF6-mediated unfolded protein response | GO:0036500 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| mammary gland duct morphogenesis | GO:0060603 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| desmosome organization | GO:0002934 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| positive regulation of T cell apoptotic process | GO:0070234 | 1 / 9 | 415× | 2.41e-3 | 2.32e-2 ✓ sig. |
| osmosensory signaling pathway | GO:0007231 | 1 / 9 | 415× | 2.41e-3 | 2.32e-2 ✓ sig. |
| regulation of cholesterol biosynthetic process | GO:0045540 | 1 / 12 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| amelogenesis | GO:0097186 | 1 / 12 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| membrane protein intracellular domain proteolysis | GO:0031293 | 1 / 14 | 267× | 3.74e-3 | 2.90e-2 ✓ sig. |