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 230
7
Diseases
91
Unique genes
0.092
Avg. similarity score
Cutaneous mastocytosis
Most-connected disease (5 links)
Disease
Searched: isovaleric acidemia
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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isovaleric acidemia
Cutaneous mastocytosis
Mastocytosis
Secondary malignant neoplasm
Systemic mastocytosis
Sickle cell anemia
Intellectual developmental disorder growth seizures
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cutaneous mastocytosis | 5 | 5 | 17 |
| Mastocytosis | 5 | 5 | 28 |
| Secondary malignant neoplasm | 5 | 5 | 19 |
| Systemic mastocytosis | 5 | 5 | 23 |
| Sickle cell anemia | 4 | 4 | 28 |
| Intellectual developmental disorder growth seizures | 3 | 3 | 1 |
| isovaleric acidemia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HBE1 | 5 / 7 | Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more |
| HBG2 | 5 / 7 | Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more |
| OR51B5 | 5 / 7 | Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more |
| ABCA2 | 4 / 7 | Cutaneous mastocytosis, Intellectual developmental disorder growth seizures, Mastocytosis, Systemic mastocytosis |
| KIT | 3 / 7 | Cutaneous mastocytosis, Mastocytosis, Systemic mastocytosis |
| OR51Q1 | 3 / 7 | Cutaneous mastocytosis, Mastocytosis, Systemic mastocytosis |
| CLIC1 | 2 / 7 | Mastocytosis, Systemic mastocytosis |
| CYP2B6 | 2 / 7 | Cutaneous mastocytosis, Mastocytosis |
| IVD | 2 / 7 | isovaleric acidemia, Secondary malignant neoplasm |
| MOCS1 | 2 / 7 | Mastocytosis, Systemic mastocytosis |
| MSH5 | 2 / 7 | Mastocytosis, Systemic mastocytosis |
| PDE4DIP | 2 / 7 | Cutaneous mastocytosis, Mastocytosis |
| RPTN | 2 / 7 | Cutaneous mastocytosis, Mastocytosis |
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 ⇵ |
|---|---|---|---|---|---|
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 2 / 101 | 29.7× | 1.90e-3 | 2.19e-2 ✓ sig. |
| Caspase activation via Dependence Receptors in the absence of ligand | Reactome | 1 / 4 | 375× | 2.66e-3 | 2.83e-2 ✓ sig. |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 375× | 2.66e-3 | 2.83e-2 ✓ sig. |
| Pathways in cancer | KEGG | 3 / 533 | 8.4× | 4.12e-3 | 3.85e-2 ✓ sig. |
| Release of Hh-Np from the secreting cell | Reactome | 1 / 7 | 214× | 4.65e-3 | 4.18e-2 ✓ sig. |
| Ligand-receptor interactions | Reactome | 1 / 7 | 214× | 4.65e-3 | 4.18e-2 ✓ sig. |
| Netrin-1 signaling | Reactome | 1 / 8 | 188× | 5.32e-3 | 4.56e-2 ✓ sig. |
| Advanced glycosylation endproduct receptor signaling | Reactome | 1 / 8 | 188× | 5.32e-3 | 4.56e-2 ✓ sig. |
| Axon guidance | KEGG | 2 / 183 | 16.4× | 6.09e-3 | 4.98e-2 ✓ sig. |
| DCC mediated attractive signaling | Reactome | 1 / 11 | 136× | 7.31e-3 | 5.62e-2 |
| Extracellular matrix organization | Reactome | 1 / 15 | 100× | 9.95e-3 | 6.82e-2 |
| Anchoring fibril formation | Reactome | 1 / 15 | 100× | 9.95e-3 | 6.82e-2 |
| Activation of SMO | Reactome | 1 / 18 | 83.4× | 1.19e-2 | 7.61e-2 |
| Crosslinking of collagen fibrils | Reactome | 1 / 18 | 83.4× | 1.19e-2 | 7.61e-2 |
| NCAM1 interactions | Reactome | 1 / 21 | 71.5× | 1.39e-2 | 8.31e-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 ⇵ |
|---|---|---|---|---|---|
| 'de novo' UMP biosynthetic process | GO:0044205 | 3 / 3 | 205× | 1.12e-7 | 1.34e-5 ✓ sig. |
| UDP biosynthetic process | GO:0006225 | 3 / 5 | 123× | 1.11e-6 | 9.10e-5 ✓ sig. |
| system process | GO:0003008 | 5 / 41 | 25.0× | 1.60e-6 | 1.22e-4 ✓ sig. |
| 'de novo' pyrimidine nucleobase biosynthetic process | GO:0006207 | 3 / 6 | 103× | 2.21e-6 | 1.59e-4 ✓ sig. |
| pyrimidine nucleotide biosynthetic process | GO:0006221 | 3 / 9 | 68.5× | 9.19e-6 | 4.98e-4 ✓ sig. |
| response to vitamin B2 | GO:0033274 | 2 / 2 | 205× | 2.35e-5 | 1.03e-3 ✓ sig. |
| smooth muscle hyperplasia | GO:0014806 | 2 / 2 | 205× | 2.35e-5 | 1.03e-3 ✓ sig. |
| response to xenobiotic stimulus | GO:0009410 | 8 / 248 | 6.6× | 2.83e-5 | 1.18e-3 ✓ sig. |
| carbon dioxide transport | GO:0015670 | 3 / 13 | 47.4× | 3.08e-5 | 1.26e-3 ✓ sig. |
| cellular response to lipid | GO:0071396 | 4 / 38 | 21.6× | 3.42e-5 | 1.37e-3 ✓ sig. |
| response to hydrogen peroxide | GO:0042542 | 4 / 39 | 21.1× | 3.80e-5 | 1.49e-3 ✓ sig. |
| oxygen transport | GO:0015671 | 3 / 17 | 36.2× | 7.23e-5 | 2.43e-3 ✓ sig. |
| negative regulation of systemic arterial blood pressure | GO:0003085 | 3 / 18 | 34.2× | 8.65e-5 | 2.78e-3 ✓ sig. |
| vasodilation | GO:0042311 | 4 / 50 | 16.4× | 1.02e-4 | 3.14e-3 ✓ sig. |
| positive regulation of protein-containing complex assembly | GO:0031334 | 4 / 50 | 16.4× | 1.02e-4 | 3.14e-3 ✓ sig. |