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 515
5
Diseases
8
Unique genes
0.235
Avg. similarity score
Giant lymph node hyperplasia
Most-connected disease (4 links)
Disease
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Giant lymph node hyperplasia
Adams-oliver syndrome
Limb, scalp and skull defects
Ventricular outflow obstruction
Autoinflammation, immune dysregulation, and eosinophilia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Giant lymph node hyperplasia | 4 | 4 | 2 |
| Adams-oliver syndrome | 3 | 3 | 6 |
| Limb, scalp and skull defects | 3 | 3 | 1 |
| Ventricular outflow obstruction | 3 | 3 | 2 |
| Autoinflammation, immune dysregulation, and eosinophilia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NOTCH1 | 4 / 5 | Adams-oliver syndrome, Giant lymph node hyperplasia, Limb, scalp and skull defects, Ventricular outflow obstruction |
| JAK1 | 2 / 5 | Autoinflammation, immune dysregulation, and eosinophilia, Giant lymph node hyperplasia |
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 ⇵ |
|---|---|---|---|---|---|
| Th1 and Th2 cell differentiation | KEGG | 4 / 93 | 64.6× | 2.30e-7 | 1.17e-5 ✓ sig. |
| Constitutive Signaling by NOTCH1 PEST Domain Mutants | Reactome | 3 / 58 | 77.7× | 5.88e-6 | 1.88e-4 ✓ sig. |
| Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants | Reactome | 3 / 58 | 77.7× | 5.88e-6 | 1.88e-4 ✓ sig. |
| Notch signaling pathway | KEGG | 3 / 62 | 72.6× | 7.20e-6 | 2.23e-4 ✓ sig. |
| Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant | Reactome | 2 / 7 | 429× | 8.14e-6 | 2.46e-4 ✓ sig. |
| NOTCH1 Intracellular Domain Regulates Transcription | Reactome | 2 / 13 | 231× | 3.02e-5 | 7.28e-4 ✓ sig. |
| RUNX3 regulates NOTCH signaling | Reactome | 2 / 14 | 214× | 3.52e-5 | 8.26e-4 ✓ sig. |
| Constitutive Signaling by NOTCH1 HD Domain Mutants | Reactome | 2 / 15 | 200× | 4.06e-5 | 9.25e-4 ✓ sig. |
| NOTCH4 Intracellular Domain Regulates Transcription | Reactome | 2 / 17 | 177× | 5.25e-5 | 1.13e-3 ✓ sig. |
| NOTCH3 Intracellular Domain Regulates Transcription | Reactome | 2 / 18 | 167× | 5.91e-5 | 1.25e-3 ✓ sig. |
| Notch-HLH transcription pathway | Reactome | 2 / 28 | 107× | 1.46e-4 | 2.55e-3 ✓ sig. |
| Pre-NOTCH Transcription and Translation | Reactome | 2 / 31 | 96.9× | 1.79e-4 | 3.01e-3 ✓ sig. |
| Human papillomavirus infection | KEGG | 3 / 333 | 13.5× | 1.07e-3 | 1.19e-2 ✓ sig. |
| Signaling by Insulin receptor | Reactome | 1 / 2 | 751× | 1.33e-3 | 1.41e-2 ✓ sig. |
| Endocrine resistance | KEGG | 2 / 99 | 30.3× | 1.82e-3 | 1.78e-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 ⇵ |
|---|---|---|---|---|---|
| ventricular trabecula myocardium morphogenesis | GO:0003222 | 3 / 15 | 467× | 2.34e-8 | 3.70e-6 ✓ sig. |
| blood vessel lumenization | GO:0072554 | 2 / 2 | 2,336× | 1.60e-7 | 1.89e-5 ✓ sig. |
| endocardium morphogenesis | GO:0003160 | 2 / 2 | 2,336× | 1.60e-7 | 1.89e-5 ✓ sig. |
| auditory receptor cell fate commitment | GO:0009912 | 2 / 3 | 1,557× | 4.81e-7 | 4.72e-5 ✓ sig. |
| regulation of cell adhesion involved in heart morphogenesis | GO:0061344 | 2 / 3 | 1,557× | 4.81e-7 | 4.72e-5 ✓ sig. |
| endocardium development | GO:0003157 | 2 / 5 | 934× | 1.60e-6 | 1.27e-4 ✓ sig. |
| epidermal cell fate specification | GO:0009957 | 2 / 5 | 934× | 1.60e-6 | 1.27e-4 ✓ sig. |
| cardiac atrium morphogenesis | GO:0003209 | 2 / 6 | 779× | 2.40e-6 | 1.76e-4 ✓ sig. |
| pericardium morphogenesis | GO:0003344 | 2 / 7 | 667× | 3.36e-6 | 2.30e-4 ✓ sig. |
| positive regulation of transcription of Notch receptor target | GO:0007221 | 2 / 7 | 667× | 3.36e-6 | 2.30e-4 ✓ sig. |
| dorsal aorta morphogenesis | GO:0035912 | 2 / 8 | 584× | 4.48e-6 | 2.90e-4 ✓ sig. |
| cardiac ventricle morphogenesis | GO:0003208 | 2 / 10 | 467× | 7.20e-6 | 4.22e-4 ✓ sig. |
| cardiac left ventricle morphogenesis | GO:0003214 | 2 / 11 | 425× | 8.80e-6 | 4.92e-4 ✓ sig. |
| cardiac muscle cell myoblast differentiation | GO:0060379 | 2 / 11 | 425× | 8.80e-6 | 4.92e-4 ✓ sig. |
| epithelial to mesenchymal transition involved in endocardial cushion formation | GO:0003198 | 2 / 13 | 359× | 1.25e-5 | 6.46e-4 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Autoinflammation, immune dysregulation, and eosinophilia | Giant lymph node hyperplasia | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Giant lymph node hyperplasia | Limb, scalp and skull defects | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Limb, scalp and skull defects | Ventricular outflow obstruction | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Giant lymph node hyperplasia | Ventricular outflow obstruction | 0.250 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Adams-oliver syndrome | Limb, scalp and skull defects | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Adams-oliver syndrome | Ventricular outflow obstruction | 0.125 | 1 | 7.75e-4 | 1.25e-3 ✓ sig. |
| Adams-oliver syndrome | Giant lymph node hyperplasia | 0.125 | 1 | 7.75e-4 | 1.25e-3 ✓ sig. |