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 528
5
Diseases
7
Unique genes
0.286
Avg. similarity score
Porphyria cutanea tarda
Most-connected disease (4 links)
Disease
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Porphyria cutanea tarda
Coproporphyria
Harderoporphyria
Hereditary coproporphyria
Hepatoerythropoietic porphyria
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Porphyria cutanea tarda | 4 | 4 | 7 |
| Coproporphyria | 3 | 3 | 1 |
| Harderoporphyria | 3 | 3 | 1 |
| Hereditary coproporphyria | 3 | 3 | 1 |
| Hepatoerythropoietic porphyria | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CPOX | 4 / 5 | Coproporphyria, Harderoporphyria, Hereditary coproporphyria, Porphyria cutanea tarda |
| UROD | 2 / 5 | Hepatoerythropoietic porphyria, Porphyria cutanea tarda |
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 ⇵ |
|---|---|---|---|---|---|
| Heme biosynthesis | Reactome | 3 / 14 | 368× | 4.40e-8 | 2.73e-6 ✓ sig. |
| Biosynthesis of protectins | Reactome | 2 / 4 | 858× | 1.75e-6 | 6.76e-5 ✓ sig. |
| Porphyrin metabolism | KEGG | 3 / 46 | 112× | 1.82e-6 | 6.98e-5 ✓ sig. |
| Chemical carcinogenesis - DNA adducts | KEGG | 3 / 70 | 73.5× | 6.53e-6 | 2.04e-4 ✓ sig. |
| Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) | Reactome | 2 / 8 | 429× | 8.14e-6 | 2.46e-4 ✓ sig. |
| Metabolism of xenobiotics by cytochrome P450 | KEGG | 3 / 79 | 65.2× | 9.41e-6 | 2.77e-4 ✓ sig. |
| Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) | Reactome | 2 / 9 | 381× | 1.05e-5 | 3.02e-4 ✓ sig. |
| Metabolic pathways | KEGG | 6 / 1,563 | 6.6× | 3.00e-5 | 7.24e-4 ✓ sig. |
| Biosynthesis of cofactors | KEGG | 3 / 154 | 33.4× | 6.97e-5 | 1.42e-3 ✓ sig. |
| Chemical carcinogenesis - receptor activation | KEGG | 3 / 215 | 23.9× | 1.88e-4 | 3.12e-3 ✓ sig. |
| Chemical carcinogenesis - reactive oxygen species | KEGG | 3 / 227 | 22.7× | 2.21e-4 | 3.55e-3 ✓ sig. |
| Tryptophan metabolism | KEGG | 2 / 42 | 81.7× | 2.48e-4 | 3.89e-3 ✓ sig. |
| Steroid hormone biosynthesis | KEGG | 2 / 63 | 54.5× | 5.59e-4 | 7.29e-3 ✓ sig. |
| Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 7.52e-3 ✓ sig. |
| Retinol metabolism | KEGG | 2 / 68 | 50.5× | 6.51e-4 | 8.19e-3 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| porphyrin-containing compound metabolic process | GO:0006778 | 3 / 7 | 1,144× | 1.13e-9 | 2.57e-7 ✓ sig. |
| protoporphyrinogen IX biosynthetic process | GO:0006782 | 3 / 9 | 890× | 2.70e-9 | 5.54e-7 ✓ sig. |
| heme O biosynthetic process | GO:0048034 | 3 / 9 | 890× | 2.70e-9 | 5.54e-7 ✓ sig. |
| heme A biosynthetic process | GO:0006784 | 3 / 10 | 801× | 3.86e-9 | 7.61e-7 ✓ sig. |
| heme B biosynthetic process | GO:0006785 | 3 / 10 | 801× | 3.86e-9 | 7.61e-7 ✓ sig. |
| response to arsenic-containing substance | GO:0046685 | 3 / 11 | 728× | 5.30e-9 | 1.01e-6 ✓ sig. |
| porphyrin-containing compound biosynthetic process | GO:0006779 | 3 / 11 | 728× | 5.30e-9 | 1.01e-6 ✓ sig. |
| response to iron ion | GO:0010039 | 3 / 18 | 445× | 2.62e-8 | 4.09e-6 ✓ sig. |
| heme biosynthetic process | GO:0006783 | 3 / 27 | 297× | 9.38e-8 | 1.20e-5 ✓ sig. |
| xenobiotic catabolic process | GO:0042178 | 3 / 28 | 286× | 1.05e-7 | 1.32e-5 ✓ sig. |
| dibenzo-p-dioxin metabolic process | GO:0018894 | 2 / 3 | 1,780× | 3.61e-7 | 3.69e-5 ✓ sig. |
| olefinic compound metabolic process | GO:0120254 | 2 / 4 | 1,335× | 7.21e-7 | 6.58e-5 ✓ sig. |
| response to herbicide | GO:0009635 | 2 / 5 | 1,068× | 1.20e-6 | 9.99e-5 ✓ sig. |
| response to methylmercury | GO:0051597 | 2 / 6 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| steroid catabolic process | GO:0006706 | 2 / 7 | 763× | 2.52e-6 | 1.83e-4 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Coproporphyria | Hereditary coproporphyria | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Coproporphyria | Harderoporphyria | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Harderoporphyria | Hereditary coproporphyria | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Coproporphyria | Porphyria cutanea tarda | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Harderoporphyria | Porphyria cutanea tarda | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Hepatoerythropoietic porphyria | Porphyria cutanea tarda | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Hereditary coproporphyria | Porphyria cutanea tarda | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |