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 524
5
Diseases
5
Unique genes
0.367
Avg. similarity score
Absence of fingerprints-congenital milia syndrome
Most-connected disease (4 links)
Disease
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Absence of fingerprints-congenital milia syndrome
Adermatoglyphia
Basan syndrome
Huriez syndrome
Palmoplantar keratoderma
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Absence of fingerprints-congenital milia syndrome | 4 | 4 | 1 |
| Adermatoglyphia | 4 | 4 | 1 |
| Basan syndrome | 4 | 4 | 1 |
| Huriez syndrome | 4 | 4 | 1 |
| Palmoplantar keratoderma | 4 | 4 | 5 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SMARCAD1 | 5 / 5 | Absence of fingerprints-congenital milia syndrome, Adermatoglyphia, Basan syndrome, Huriez syndrome and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Staphylococcus aureus infection | KEGG | 2 / 99 | 48.5× | 6.62e-4 | 8.28e-3 ✓ sig. |
| Formation of the cornified envelope | Reactome | 2 / 130 | 37.0× | 1.14e-3 | 1.25e-2 ✓ sig. |
| Estrogen signaling pathway | KEGG | 2 / 139 | 34.6× | 1.30e-3 | 1.38e-2 ✓ sig. |
| Keratinization | Reactome | 2 / 152 | 31.6× | 1.55e-3 | 1.58e-2 ✓ sig. |
| Type I hemidesmosome assembly | Reactome | 1 / 11 | 218× | 4.57e-3 | 3.44e-2 ✓ sig. |
| Cargo concentration in the ER | Reactome | 1 / 33 | 72.8× | 1.37e-2 | 6.87e-2 |
| COPII-mediated vesicle transport | Reactome | 1 / 68 | 35.3× | 2.80e-2 | 1.04e-1 |
| MHC class II antigen presentation | Reactome | 1 / 123 | 19.5× | 5.02e-2 | 1.45e-1 |
| Lysosome | KEGG | 1 / 133 | 18.1× | 5.42e-2 | 1.51e-1 |
| Apoptosis | KEGG | 1 / 137 | 17.5× | 5.58e-2 | 1.54e-1 |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 1 / 144 | 16.7× | 5.85e-2 | 1.58e-1 |
| Neuroactive ligand-receptor interaction | KEGG | 1 / 370 | 6.5× | 1.45e-1 | 2.70e-1 |
| Neutrophil degranulation | Reactome | 1 / 480 | 5.0× | 1.85e-1 | 3.15e-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 ⇵ |
|---|---|---|---|---|---|
| morphogenesis of an epithelium | GO:0002009 | 2 / 51 | 147× | 7.26e-5 | 2.44e-3 ✓ sig. |
| keratinocyte differentiation | GO:0030216 | 2 / 69 | 108× | 1.33e-4 | 3.80e-3 ✓ sig. |
| intermediate filament organization | GO:0045109 | 2 / 70 | 107× | 1.37e-4 | 3.88e-3 ✓ sig. |
| urokinase plasminogen activator signaling pathway | GO:0038195 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| chromosome separation | GO:0051304 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| regulation of DNA recombination | GO:0000018 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| positive regulation of epidermis development | GO:0045684 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| intermediate filament bundle assembly | GO:0045110 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| positive regulation of proteolysis involved in protein catabolic process | GO:1903052 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| positive regulation of microglial cell activation | GO:1903980 | 1 / 9 | 415× | 2.41e-3 | 2.32e-2 ✓ sig. |
| negative regulation of myelination | GO:0031642 | 1 / 9 | 415× | 2.41e-3 | 2.32e-2 ✓ sig. |
| cell activation | GO:0001775 | 1 / 11 | 340× | 2.94e-3 | 2.58e-2 ✓ sig. |
| neuromuscular process controlling posture | GO:0050884 | 1 / 15 | 249× | 4.01e-3 | 3.01e-2 ✓ sig. |
| DNA double-strand break processing | GO:0000729 | 1 / 15 | 249× | 4.01e-3 | 3.01e-2 ✓ sig. |
| protein heterotetramerization | GO:0051290 | 1 / 16 | 234× | 4.27e-3 | 3.09e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Absence of fingerprints-congenital milia syndrome | Huriez syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Absence of fingerprints-congenital milia syndrome | Basan syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Absence of fingerprints-congenital milia syndrome | Adermatoglyphia | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Adermatoglyphia | Huriez syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Adermatoglyphia | Basan syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Basan syndrome | Huriez syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Absence of fingerprints-congenital milia syndrome | Palmoplantar keratoderma | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Adermatoglyphia | Palmoplantar keratoderma | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Basan syndrome | Palmoplantar keratoderma | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Huriez syndrome | Palmoplantar keratoderma | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |