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 431
5
Diseases
11
Unique genes
0.302
Avg. similarity score
Hereditary xerocytosis
Most-connected disease (4 links)
Disease
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Hereditary xerocytosis
Xerocytosis
dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema
obsolete PIEZO1-related generalized lymphatic dysplasia with non-immune hydrops fetalis
Distal renal tubular acidosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Hereditary xerocytosis | 4 | 4 | 3 |
| Xerocytosis | 4 | 4 | 3 |
| dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema | 3 | 3 | 1 |
| obsolete PIEZO1-related generalized lymphatic dysplasia with non-immune hydrops fetalis | 3 | 3 | 1 |
| Distal renal tubular acidosis | 2 | 2 | 9 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PIEZO1 | 4 / 5 | dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema, Hereditary xerocytosis, obsolete PIEZO1-related generalized lymphatic dysplasia with non-immune hydrops fetalis, Xerocytosis |
| SLC4A1 | 3 / 5 | Distal renal tubular acidosis, Hereditary xerocytosis, Xerocytosis |
| KCNN4 | 2 / 5 | Hereditary xerocytosis, Xerocytosis |
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 ⇵ |
|---|---|---|---|---|---|
| Collecting duct acid secretion | KEGG | 4 / 28 | 156× | 7.71e-9 | 6.98e-7 ✓ sig. |
| Bicarbonate transporters | Reactome | 3 / 10 | 328× | 6.84e-8 | 4.71e-6 ✓ sig. |
| Ion channel transport | Reactome | 3 / 24 | 136× | 1.14e-6 | 5.49e-5 ✓ sig. |
| Insulin receptor recycling | Reactome | 3 / 26 | 126× | 1.47e-6 | 6.81e-5 ✓ sig. |
| Transferrin endocytosis and recycling | Reactome | 3 / 31 | 106× | 2.53e-6 | 1.08e-4 ✓ sig. |
| ROS and RNS production in phagocytes | Reactome | 3 / 34 | 96.3× | 3.37e-6 | 1.37e-4 ✓ sig. |
| Vibrio cholerae infection | KEGG | 3 / 51 | 64.2× | 1.16e-5 | 3.80e-4 ✓ sig. |
| Epithelial cell signaling in Helicobacter pylori infection | KEGG | 3 / 71 | 46.1× | 3.16e-5 | 8.71e-4 ✓ sig. |
| Synaptic vesicle cycle | KEGG | 3 / 79 | 41.5× | 4.35e-5 | 1.14e-3 ✓ sig. |
| Rheumatoid arthritis | KEGG | 3 / 95 | 34.5× | 7.56e-5 | 1.78e-3 ✓ sig. |
| Oxidative phosphorylation | KEGG | 3 / 137 | 23.9× | 2.24e-4 | 4.28e-3 ✓ sig. |
| Phagosome | KEGG | 3 / 155 | 21.1× | 3.22e-4 | 5.68e-3 ✓ sig. |
| Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) | Reactome | 1 / 1 | 1,092× | 9.16e-4 | 1.27e-2 ✓ sig. |
| Amino acids regulate mTORC1 | Reactome | 2 / 55 | 39.7× | 1.10e-3 | 1.46e-2 ✓ sig. |
| Human papillomavirus infection | KEGG | 3 / 333 | 9.8× | 2.95e-3 | 3.04e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| monoatomic ion transport | GO:0006811 | 8 / 667 | 20.4× | 3.79e-10 | 9.38e-8 ✓ sig. |
| monoatomic anion transport | GO:0006820 | 3 / 19 | 268× | 1.46e-7 | 1.67e-5 ✓ sig. |
| regulation of intracellular pH | GO:0051453 | 3 / 28 | 182× | 4.93e-7 | 4.63e-5 ✓ sig. |
| bicarbonate transport | GO:0015701 | 3 / 33 | 154× | 8.20e-7 | 7.06e-5 ✓ sig. |
| renal tubular secretion | GO:0097254 | 2 / 3 | 1,133× | 9.45e-7 | 7.93e-5 ✓ sig. |
| pH reduction | GO:0045851 | 2 / 7 | 485× | 6.60e-6 | 3.74e-4 ✓ sig. |
| chloride transmembrane transport | GO:1902476 | 3 / 114 | 44.7× | 3.52e-5 | 1.38e-3 ✓ sig. |
| inorganic anion transport | GO:0015698 | 2 / 17 | 200× | 4.26e-5 | 1.60e-3 ✓ sig. |
| synaptic vesicle lumen acidification | GO:0097401 | 2 / 18 | 189× | 4.80e-5 | 1.74e-3 ✓ sig. |
| regulation of pH | GO:0006885 | 2 / 21 | 162× | 6.58e-5 | 2.21e-3 ✓ sig. |
| vacuolar acidification | GO:0007035 | 2 / 23 | 148× | 7.92e-5 | 2.54e-3 ✓ sig. |
| proton transmembrane transport | GO:1902600 | 3 / 181 | 28.2× | 1.39e-4 | 3.86e-3 ✓ sig. |
| monoatomic anion transmembrane transport | GO:0098656 | 2 / 40 | 84.9× | 2.43e-4 | 5.79e-3 ✓ sig. |
| regulation of macroautophagy | GO:0016241 | 2 / 57 | 59.6× | 4.94e-4 | 9.48e-3 ✓ sig. |
| pH elevation | GO:0045852 | 1 / 1 | 1,699× | 5.89e-4 | 1.07e-2 ✓ sig. |