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 215
8
Diseases
26
Unique genes
0.216
Avg. similarity score
Bladder neck obstruction
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Bladder neck obstruction
Carcinoma in situ
Urinary bladder neck obstruction
Curling ulcer
Pericardial effusion
Diffuse gastric adenocarcinoma
Ovarian diseases
severe combined immunodeficiency due to LAT deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bladder neck obstruction | 4 | 4 | 2 |
| Carcinoma in situ | 4 | 4 | 1 |
| Urinary bladder neck obstruction | 4 | 4 | 1 |
| Curling ulcer | 3 | 3 | 6 |
| Pericardial effusion | 3 | 3 | 4 |
| Diffuse gastric adenocarcinoma | 2 | 2 | 16 |
| Ovarian diseases | 1 | 1 | 3 |
| severe combined immunodeficiency due to LAT deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PTGS2 | 5 / 8 | Bladder neck obstruction, Carcinoma in situ, Curling ulcer, Pericardial effusion and 1 more |
| ABO | 2 / 8 | Curling ulcer, Diffuse gastric adenocarcinoma |
| CYP19A1 | 2 / 8 | Bladder neck obstruction, Ovarian diseases |
| LAT | 2 / 8 | Diffuse gastric adenocarcinoma, severe combined immunodeficiency due to LAT deficiency |
| PSCA | 2 / 8 | Curling ulcer, Diffuse gastric adenocarcinoma |
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 ⇵ |
|---|---|---|---|---|---|
| Ovarian steroidogenesis | KEGG | 4 / 52 | 35.5× | 4.35e-6 | 1.70e-4 ✓ sig. |
| Leishmaniasis | KEGG | 3 / 78 | 17.8× | 6.15e-4 | 9.38e-3 ✓ sig. |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 3 / 108 | 12.8× | 1.58e-3 | 1.92e-2 ✓ sig. |
| Defective CYP19A1 causes Aromatase excess syndrome (AEXS) | Reactome | 1 / 1 | 462× | 2.16e-3 | 2.42e-2 ✓ sig. |
| Biosynthesis of EPA-derived SPMs | Reactome | 1 / 1 | 462× | 2.16e-3 | 2.42e-2 ✓ sig. |
| Biosynthesis of DPAn-3 SPMs | Reactome | 1 / 1 | 462× | 2.16e-3 | 2.42e-2 ✓ sig. |
| Signaling by PDGF | Reactome | 2 / 33 | 28.0× | 2.28e-3 | 2.52e-2 ✓ sig. |
| Oxytocin signaling pathway | KEGG | 3 / 154 | 9.0× | 4.33e-3 | 3.98e-2 ✓ sig. |
| Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives | Reactome | 1 / 2 | 231× | 4.33e-3 | 3.98e-2 ✓ sig. |
| Influenza Virus Induced Apoptosis | Reactome | 1 / 2 | 231× | 4.33e-3 | 3.98e-2 ✓ sig. |
| phospho-PLA2 pathway | Reactome | 1 / 2 | 231× | 4.33e-3 | 3.98e-2 ✓ sig. |
| TGFBR2 MSI Frameshift Mutants in Cancer | Reactome | 1 / 2 | 231× | 4.33e-3 | 3.98e-2 ✓ sig. |
| Malaria | KEGG | 2 / 50 | 18.5× | 5.18e-3 | 4.47e-2 ✓ sig. |
| Biosynthesis of DHA-derived SPMs | Reactome | 1 / 3 | 154× | 6.48e-3 | 5.19e-2 |
| ABO blood group biosynthesis | Reactome | 1 / 3 | 154× | 6.48e-3 | 5.19e-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 ⇵ |
|---|---|---|---|---|---|
| prostaglandin secretion | GO:0032310 | 2 / 5 | 287× | 1.86e-5 | 8.45e-4 ✓ sig. |
| response to hypoxia | GO:0001666 | 4 / 176 | 16.3× | 9.67e-5 | 2.95e-3 ✓ sig. |
| regulation of cell population proliferation | GO:0042127 | 4 / 201 | 14.3× | 1.61e-4 | 4.33e-3 ✓ sig. |
| prostaglandin biosynthetic process | GO:0001516 | 2 / 17 | 84.6× | 2.50e-4 | 5.92e-3 ✓ sig. |
| regulation of JNK cascade | GO:0046328 | 2 / 23 | 62.5× | 4.63e-4 | 9.08e-3 ✓ sig. |
| ventricular cardiac muscle tissue morphogenesis | GO:0055010 | 2 / 24 | 59.9× | 5.04e-4 | 9.63e-3 ✓ sig. |
| animal organ regeneration | GO:0031100 | 2 / 28 | 51.3× | 6.88e-4 | 1.18e-2 ✓ sig. |
| cell-cell junction organization | GO:0045216 | 2 / 29 | 49.6× | 7.38e-4 | 1.24e-2 ✓ sig. |
| prostaglandin metabolic process | GO:0006693 | 2 / 30 | 47.9× | 7.91e-4 | 1.30e-2 ✓ sig. |
| positive regulation of vascular endothelial growth factor production | GO:0010575 | 2 / 32 | 44.9× | 9.00e-4 | 1.41e-2 ✓ sig. |
| lamellipodium assembly | GO:0030032 | 2 / 36 | 39.9× | 1.14e-3 | 1.64e-2 ✓ sig. |
| positive regulation of cell migration involved in sprouting angiogenesis | GO:0090050 | 2 / 37 | 38.9× | 1.20e-3 | 1.69e-2 ✓ sig. |
| sprouting angiogenesis | GO:0002040 | 2 / 37 | 38.9× | 1.20e-3 | 1.69e-2 ✓ sig. |
| mammary gland development | GO:0030879 | 2 / 37 | 38.9× | 1.20e-3 | 1.69e-2 ✓ sig. |
| positive regulation of cell fate determination | GO:1905935 | 1 / 1 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Curling ulcer | Diffuse gastric adenocarcinoma | 0.095 | 2 | 1.51e-5 | 7.72e-5 ✓ sig. |
| Carcinoma in situ | Urinary bladder neck obstruction | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Bladder neck obstruction | Carcinoma in situ | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Bladder neck obstruction | Urinary bladder neck obstruction | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Carcinoma in situ | Pericardial effusion | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Pericardial effusion | Urinary bladder neck obstruction | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Bladder neck obstruction | Ovarian diseases | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Carcinoma in situ | Curling ulcer | 0.143 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Curling ulcer | Urinary bladder neck obstruction | 0.143 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Bladder neck obstruction | Pericardial effusion | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |
| Diffuse gastric adenocarcinoma | severe combined immunodeficiency due to LAT deficiency | 0.059 | 1 | 1.04e-3 | 1.72e-3 ✓ sig. |