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 359
6
Diseases
6
Unique genes
0.218
Avg. similarity score
Magnesium metabolism disorder
Most-connected disease (5 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Magnesium metabolism disorder
Tetany
hypomagnesemia, seizures, and intellectual disability 1
Intestinal hypomagnesemia
renal hypomagnesemia 3
renal hypomagnesemia 4
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Magnesium metabolism disorder | 5 | 5 | 5 |
| Tetany | 2 | 2 | 1 |
| hypomagnesemia, seizures, and intellectual disability 1 | 2 | 2 | 1 |
| Intestinal hypomagnesemia | 1 | 1 | 2 |
| renal hypomagnesemia 3 | 1 | 1 | 1 |
| renal hypomagnesemia 4 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CNNM2 | 3 / 6 | hypomagnesemia, seizures, and intellectual disability 1, Magnesium metabolism disorder, Tetany |
| CLDN16 | 2 / 6 | Magnesium metabolism disorder, renal hypomagnesemia 3 |
| EGF | 2 / 6 | Magnesium metabolism disorder, renal hypomagnesemia 4 |
| TRPM6 | 2 / 6 | Intestinal hypomagnesemia, Magnesium metabolism disorder |
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 ⇵ |
|---|---|---|---|---|---|
| Mineral absorption | KEGG | 3 / 61 | 98.4× | 2.47e-6 | 1.06e-4 ✓ sig. |
| TRP channels | Reactome | 2 / 28 | 143× | 7.82e-5 | 1.83e-3 ✓ sig. |
| Salivary secretion | KEGG | 2 / 93 | 43.0× | 8.72e-4 | 1.22e-2 ✓ sig. |
| Hepatitis C | KEGG | 2 / 159 | 25.2× | 2.52e-3 | 2.71e-2 ✓ sig. |
| Inhibition of Signaling by Overexpressed EGFR | Reactome | 1 / 8 | 250× | 3.99e-3 | 3.77e-2 ✓ sig. |
| EGFR interacts with phospholipase C-gamma | Reactome | 1 / 9 | 222× | 4.49e-3 | 4.08e-2 ✓ sig. |
| Signaling by ERBB4 | Reactome | 1 / 11 | 182× | 5.48e-3 | 4.65e-2 ✓ sig. |
| Signaling by EGFR | Reactome | 1 / 11 | 182× | 5.48e-3 | 4.65e-2 ✓ sig. |
| ERBB2 Activates PTK6 Signaling | Reactome | 1 / 13 | 154× | 6.48e-3 | 5.19e-2 |
| GRB2 events in EGFR signaling | Reactome | 1 / 13 | 154× | 6.48e-3 | 5.19e-2 |
| SHC1 events in EGFR signaling | Reactome | 1 / 14 | 143× | 6.98e-3 | 5.45e-2 |
| ERBB2 Regulates Cell Motility | Reactome | 1 / 15 | 133× | 7.47e-3 | 5.69e-2 |
| Constitutive Signaling by EGFRvIII | Reactome | 1 / 15 | 133× | 7.47e-3 | 5.69e-2 |
| PI3K events in ERBB2 signaling | Reactome | 1 / 16 | 125× | 7.97e-3 | 5.96e-2 |
| Signaling by ERBB2 ECD mutants | Reactome | 1 / 16 | 125× | 7.97e-3 | 5.96e-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 ⇵ |
|---|---|---|---|---|---|
| magnesium ion transmembrane transport | GO:1903830 | 3 / 17 | 550× | 1.25e-8 | 2.07e-6 ✓ sig. |
| monoatomic ion transport | GO:0006811 | 5 / 667 | 23.3× | 3.32e-7 | 3.32e-5 ✓ sig. |
| metal ion transport | GO:0030001 | 2 / 30 | 208× | 3.72e-5 | 1.44e-3 ✓ sig. |
| intercellular transport | GO:0010496 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| transmembrane transport | GO:0055085 | 3 / 557 | 16.8× | 4.93e-4 | 9.46e-3 ✓ sig. |
| parathyroid hormone secretion | GO:0035898 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| calcium ion transmembrane transport | GO:0070588 | 2 / 149 | 41.8× | 9.28e-4 | 1.44e-2 ✓ sig. |
| calcium ion transport | GO:0006816 | 2 / 157 | 39.7× | 1.03e-3 | 1.53e-2 ✓ sig. |
| negative regulation of secretion | GO:0051048 | 1 / 4 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| positive regulation of hyaluronan biosynthetic process | GO:1900127 | 1 / 4 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| cellular hyperosmotic salinity response | GO:0071475 | 1 / 5 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| positive regulation of epithelial tube formation | GO:1905278 | 1 / 5 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| positive regulation of cerebellar granule cell precursor proliferation | GO:0021940 | 1 / 5 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| paracellular transport | GO:0160184 | 1 / 7 | 445× | 2.25e-3 | 2.41e-2 ✓ sig. |
| magnesium ion homeostasis | GO:0010960 | 1 / 8 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| hypomagnesemia, seizures, and intellectual disability 1 | Tetany | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| hypomagnesemia, seizures, and intellectual disability 1 | Magnesium metabolism disorder | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Magnesium metabolism disorder | Tetany | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Magnesium metabolism disorder | renal hypomagnesemia 4 | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Magnesium metabolism disorder | renal hypomagnesemia 3 | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Intestinal hypomagnesemia | Magnesium metabolism disorder | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |