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 625
5
Diseases
7
Unique genes
0.229
Avg. similarity score
Vitamin d dependent rickets
Most-connected disease (4 links)
Disease
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Vitamin d dependent rickets
Hypocalcemic vitamin d-dependent rickets
Peptic esophagitis
Rickets due to defect in vitamin d 25-hydroxylation
Pancreatic trypsinogen deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Vitamin d dependent rickets | 4 | 4 | 7 |
| Hypocalcemic vitamin d-dependent rickets | 3 | 3 | 3 |
| Peptic esophagitis | 2 | 2 | 1 |
| Rickets due to defect in vitamin d 25-hydroxylation | 2 | 2 | 1 |
| Pancreatic trypsinogen deficiency | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CYP2R1 | 3 / 5 | Hypocalcemic vitamin d-dependent rickets, Rickets due to defect in vitamin d 25-hydroxylation, Vitamin d dependent rickets |
| VDR | 3 / 5 | Hypocalcemic vitamin d-dependent rickets, Peptic esophagitis, Vitamin d dependent rickets |
| CYP27B1 | 2 / 5 | Hypocalcemic vitamin d-dependent rickets, Vitamin d dependent rickets |
| PRSS1 | 2 / 5 | Pancreatic trypsinogen deficiency, Vitamin d dependent rickets |
| TRB | 2 / 5 | Pancreatic trypsinogen deficiency, Vitamin d dependent rickets |
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 ⇵ |
|---|---|---|---|---|---|
| Vitamin D (calciferol) metabolism | Reactome | 3 / 11 | 468× | 2.00e-8 | 1.36e-6 ✓ sig. |
| Vitamins | Reactome | 2 / 6 | 572× | 4.36e-6 | 1.47e-4 ✓ sig. |
| Steroid biosynthesis | KEGG | 2 / 20 | 172× | 5.51e-5 | 1.18e-3 ✓ sig. |
| Defective CYP2R1 causes Rickets vitamin D-dependent 1B (VDDR1B) | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 7.52e-3 ✓ sig. |
| Defective CYP27B1 causes Rickets vitamin D-dependent 1A (VDDR1A) | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 7.52e-3 ✓ sig. |
| PDE3B signalling | Reactome | 1 / 1 | 1,716× | 5.83e-4 | 7.52e-3 ✓ sig. |
| Parathyroid hormone synthesis, secretion and action | KEGG | 2 / 115 | 29.8× | 1.85e-3 | 1.80e-2 ✓ sig. |
| Biosynthesis of maresin-like SPMs | Reactome | 1 / 6 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| Tuberculosis | KEGG | 2 / 181 | 19.0× | 4.51e-3 | 3.41e-2 ✓ sig. |
| Chemical carcinogenesis - receptor activation | KEGG | 2 / 215 | 16.0× | 6.31e-3 | 4.25e-2 ✓ sig. |
| Metabolic pathways | KEGG | 4 / 1,563 | 4.4× | 7.21e-3 | 4.64e-2 ✓ sig. |
| Aflatoxin activation and detoxification | Reactome | 1 / 19 | 90.3× | 1.10e-2 | 6.03e-2 |
| Cobalamin (Cbl, vitamin B12) transport and metabolism | Reactome | 1 / 21 | 81.7× | 1.22e-2 | 6.41e-2 |
| Xenobiotics | Reactome | 1 / 24 | 71.5× | 1.39e-2 | 6.94e-2 |
| SUMOylation of intracellular receptors | Reactome | 1 / 27 | 63.5× | 1.56e-2 | 7.44e-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 ⇵ |
|---|---|---|---|---|---|
| calcitriol biosynthetic process from calciol | GO:0036378 | 3 / 5 | 1,602× | 3.22e-10 | 8.69e-8 ✓ sig. |
| vitamin D metabolic process | GO:0042359 | 3 / 12 | 667× | 7.07e-9 | 1.31e-6 ✓ sig. |
| vitamin D biosynthetic process | GO:0042368 | 2 / 2 | 2,670× | 1.20e-7 | 1.48e-5 ✓ sig. |
| vitamin D catabolic process | GO:0042369 | 2 / 4 | 1,335× | 7.21e-7 | 6.58e-5 ✓ sig. |
| positive regulation of vitamin D receptor signaling pathway | GO:0070564 | 2 / 6 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| vitamin metabolic process | GO:0006766 | 2 / 6 | 890× | 1.80e-6 | 1.39e-4 ✓ sig. |
| positive regulation of keratinocyte differentiation | GO:0045618 | 2 / 20 | 267× | 2.28e-5 | 1.02e-3 ✓ sig. |
| decidualization | GO:0046697 | 2 / 25 | 214× | 3.59e-5 | 1.44e-3 ✓ sig. |
| response to cesium ion | GO:0010164 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| nuclear receptor-mediated bile acid signaling pathway | GO:0038185 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| negative regulation of phosphate transmembrane transport | GO:2000186 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| xenobiotic metabolic process | GO:0006805 | 2 / 120 | 44.5× | 8.41e-4 | 1.33e-2 ✓ sig. |
| apoptotic process involved in mammary gland involution | GO:0060057 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| alkaloid catabolic process | GO:0009822 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| T cell mediated cytotoxicity directed against tumor cell target | GO:0002419 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Hypocalcemic vitamin d-dependent rickets | Vitamin d dependent rickets | 0.375 | 3 | 5.65e-11 | 5.40e-10 ✓ sig. |
| Pancreatic trypsinogen deficiency | Vitamin d dependent rickets | 0.250 | 2 | 1.75e-7 | 1.18e-6 ✓ sig. |
| Hypocalcemic vitamin d-dependent rickets | Peptic esophagitis | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Hypocalcemic vitamin d-dependent rickets | Rickets due to defect in vitamin d 25-hydroxylation | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Rickets due to defect in vitamin d 25-hydroxylation | Vitamin d dependent rickets | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Peptic esophagitis | Vitamin d dependent rickets | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |