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 309
7
Diseases
159
Unique genes
0.277
Avg. similarity score
Periodontal disease
Most-connected disease (5 links)
Disease
Searched: Periodontititis, aggressive, 1
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Periodontititis, aggressive, 1
Periodontal disease
Haim-munk syndrome
Papillon-lefevre syndrome
Periodontitis 1, juvenile
Periodontitis
Paganini-miozzo syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Periodontal disease | 5 | 5 | 19 |
| Haim-munk syndrome | 4 | 4 | 1 |
| Papillon-lefevre syndrome | 4 | 4 | 1 |
| Periodontitis 1, juvenile | 4 | 4 | 1 |
| Periodontititis, aggressive, 1 | 4 | 4 | 1 |
| Periodontitis | 2 | 2 | 158 |
| Paganini-miozzo syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CTSC | 6 / 7 | Haim-munk syndrome, Papillon-lefevre syndrome, Periodontal disease, Periodontitis and 2 more |
| AAK1 | 2 / 7 | Periodontal disease, Periodontitis |
| CAMK2N1 | 2 / 7 | Periodontal disease, Periodontitis |
| CCR7 | 2 / 7 | Periodontal disease, Periodontitis |
| CFAP44 | 2 / 7 | Periodontal disease, Periodontitis |
| FCHO2 | 2 / 7 | Periodontal disease, Periodontitis |
| FKBP1C | 2 / 7 | Periodontal disease, Periodontitis |
| HS6ST2 | 2 / 7 | Paganini-miozzo syndrome, Periodontitis |
| IL6 | 2 / 7 | Periodontal disease, Periodontitis |
| ITGA4 | 2 / 7 | Periodontal disease, Periodontitis |
| KALRN | 2 / 7 | Periodontal disease, Periodontitis |
| LARP1B | 2 / 7 | Periodontal disease, Periodontitis |
| MBP | 2 / 7 | Periodontal disease, Periodontitis |
| PIK3C3 | 2 / 7 | Periodontal disease, Periodontitis |
| PPARG | 2 / 7 | Periodontal disease, Periodontitis |
| SIGLEC5 | 2 / 7 | Periodontal disease, Periodontitis |
| SMARCE1 | 2 / 7 | Periodontal disease, Periodontitis |
| SYNDIG1 | 2 / 7 | Periodontal disease, Periodontitis |
| TSEN2 | 2 / 7 | Periodontal disease, Periodontitis |
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 ⇵ |
|---|---|---|---|---|---|
| Arrhythmogenic right ventricular cardiomyopathy | KEGG | 8 / 86 | 7.0× | 1.75e-5 | 4.30e-4 ✓ sig. |
| Activation of Matrix Metalloproteinases | Reactome | 5 / 33 | 11.4× | 6.72e-5 | 1.28e-3 ✓ sig. |
| Rheumatoid arthritis | KEGG | 6 / 95 | 4.8× | 1.61e-3 | 1.55e-2 ✓ sig. |
| Hypertrophic cardiomyopathy | KEGG | 6 / 99 | 4.6× | 1.99e-3 | 1.82e-2 ✓ sig. |
| Dilated cardiomyopathy | KEGG | 6 / 105 | 4.3× | 2.68e-3 | 2.26e-2 ✓ sig. |
| Intestinal immune network for IgA production | KEGG | 4 / 50 | 6.0× | 4.24e-3 | 3.12e-2 ✓ sig. |
| Cell adhesion molecule (CAM) interaction | KEGG | 7 / 160 | 3.3× | 5.38e-3 | 3.68e-2 ✓ sig. |
| Signaling by ROBO receptors | Reactome | 2 / 12 | 12.6× | 1.05e-2 | 5.67e-2 |
| Cytoskeleton in muscle cells | KEGG | 8 / 232 | 2.6× | 1.20e-2 | 6.15e-2 |
| Defective GGT1 causes Glutathionuria (GLUTH) | Reactome | 1 / 1 | 75.5× | 1.32e-2 | 6.52e-2 |
| PTEN Loss of Function in Cancer | Reactome | 1 / 1 | 75.5× | 1.32e-2 | 6.52e-2 |
| Degradation of the extracellular matrix | Reactome | 4 / 70 | 4.3× | 1.38e-2 | 6.70e-2 |
| Transcriptional misregulation in cancer | KEGG | 7 / 198 | 2.7× | 1.62e-2 | 7.39e-2 |
| Focal adhesion | KEGG | 7 / 203 | 2.6× | 1.84e-2 | 7.95e-2 |
| Interleukin-10 signaling | Reactome | 3 / 47 | 4.8× | 2.41e-2 | 9.37e-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 ⇵ |
|---|---|---|---|---|---|
| cell-cell adhesion | GO:0098609 | 10 / 218 | 5.4× | 1.79e-5 | 8.29e-4 ✓ sig. |
| cell morphogenesis | GO:0000902 | 7 / 119 | 6.9× | 7.14e-5 | 2.36e-3 ✓ sig. |
| negative regulation of keratinocyte migration | GO:0051548 | 2 / 2 | 118× | 7.19e-5 | 2.37e-3 ✓ sig. |
| positive regulation of filopodium assembly | GO:0051491 | 4 / 30 | 15.7× | 1.16e-4 | 3.39e-3 ✓ sig. |
| synaptic vesicle clustering | GO:0097091 | 3 / 12 | 29.4× | 1.26e-4 | 3.58e-3 ✓ sig. |
| negative regulation of lipid storage | GO:0010888 | 3 / 12 | 29.4× | 1.26e-4 | 3.58e-3 ✓ sig. |
| cell adhesion | GO:0007155 | 16 / 665 | 2.8× | 1.80e-4 | 4.63e-3 ✓ sig. |
| maintenance of blood-brain barrier | GO:0035633 | 4 / 34 | 13.8× | 1.92e-4 | 4.86e-3 ✓ sig. |
| negative regulation of macrophage derived foam cell differentiation | GO:0010745 | 3 / 14 | 25.2× | 2.05e-4 | 5.09e-3 ✓ sig. |
| acute-phase response | GO:0006953 | 4 / 37 | 12.7× | 2.68e-4 | 6.12e-3 ✓ sig. |
| positive regulation of cell adhesion | GO:0045785 | 5 / 68 | 8.6× | 2.83e-4 | 6.35e-3 ✓ sig. |
| carboxylic acid catabolic process | GO:0046395 | 2 / 4 | 58.8× | 4.27e-4 | 8.38e-3 ✓ sig. |
| extracellular matrix disassembly | GO:0022617 | 4 / 47 | 10.0× | 6.77e-4 | 1.13e-2 ✓ sig. |
| muscle cell development | GO:0055001 | 3 / 23 | 15.3× | 9.45e-4 | 1.40e-2 ✓ sig. |
| cellular response to cytokine stimulus | GO:0071345 | 4 / 53 | 8.9× | 1.07e-3 | 1.49e-2 ✓ sig. |