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 312
6
Diseases
34
Unique genes
0.102
Avg. similarity score
Gallbladder neoplasms
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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Gallbladder neoplasms
Soft tissue neoplasms
amyotrophic lateral sclerosis type 19
Peritoneal disease
Conjunctival disease
Early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Gallbladder neoplasms | 4 | 4 | 25 |
| Soft tissue neoplasms | 3 | 3 | 2 |
| amyotrophic lateral sclerosis type 19 | 3 | 3 | 1 |
| Peritoneal disease | 2 | 2 | 9 |
| Conjunctival disease | 1 | 1 | 2 |
| Early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ERBB4 | 4 / 6 | amyotrophic lateral sclerosis type 19, Gallbladder neoplasms, Peritoneal disease, Soft tissue neoplasms |
| DAPK1 | 2 / 6 | Conjunctival disease, Gallbladder neoplasms |
| EPHB1 | 2 / 6 | Gallbladder neoplasms, Soft tissue neoplasms |
| UCHL1 | 2 / 6 | Early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, Gallbladder neoplasms |
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 ⇵ |
|---|---|---|---|---|---|
| Signaling by ERBB2 TMD/JMD mutants | Reactome | 5 / 22 | 80.3× | 3.40e-9 | 3.35e-7 ✓ sig. |
| Signaling by ERBB2 KD Mutants | Reactome | 5 / 25 | 70.6× | 6.83e-9 | 6.25e-7 ✓ sig. |
| ERBB2 Activates PTK6 Signaling | Reactome | 4 / 13 | 109× | 3.76e-8 | 2.77e-6 ✓ sig. |
| ERBB2 Regulates Cell Motility | Reactome | 4 / 15 | 94.2× | 7.15e-8 | 4.88e-6 ✓ sig. |
| Bladder cancer | KEGG | 5 / 41 | 43.1× | 9.32e-8 | 6.17e-6 ✓ sig. |
| PI3K events in ERBB2 signaling | Reactome | 4 / 16 | 88.3× | 9.51e-8 | 6.26e-6 ✓ sig. |
| SHC1 events in ERBB2 signaling | Reactome | 4 / 17 | 83.1× | 1.24e-7 | 7.89e-6 ✓ sig. |
| Signaling by ERBB2 | Reactome | 4 / 18 | 78.5× | 1.59e-7 | 9.80e-6 ✓ sig. |
| Downregulation of ERBB2 signaling | Reactome | 4 / 24 | 58.9× | 5.46e-7 | 2.90e-5 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 5 / 80 | 22.1× | 2.76e-6 | 1.16e-4 ✓ sig. |
| Signaling by ERBB4 | Reactome | 3 / 11 | 96.3× | 3.37e-6 | 1.37e-4 ✓ sig. |
| Gastric cancer | KEGG | 6 / 150 | 14.1× | 3.46e-6 | 1.40e-4 ✓ sig. |
| ErbB signaling pathway | KEGG | 5 / 86 | 20.5× | 3.96e-6 | 1.56e-4 ✓ sig. |
| Colorectal cancer | KEGG | 5 / 87 | 20.3× | 4.19e-6 | 1.64e-4 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 8 / 361 | 7.8× | 5.65e-6 | 2.10e-4 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of apoptotic process | GO:0043066 | 9 / 524 | 9.4× | 2.81e-7 | 2.89e-5 ✓ sig. |
| cell surface receptor protein tyrosine kinase signaling pathway | GO:0007169 | 5 / 120 | 22.9× | 2.41e-6 | 1.67e-4 ✓ sig. |
| axonogenesis | GO:0007409 | 5 / 125 | 22.0× | 2.94e-6 | 1.96e-4 ✓ sig. |
| epidermal growth factor receptor signaling pathway | GO:0007173 | 4 / 64 | 34.4× | 5.37e-6 | 3.18e-4 ✓ sig. |
| positive regulation of epithelial cell proliferation | GO:0050679 | 4 / 73 | 30.1× | 9.09e-6 | 4.85e-4 ✓ sig. |
| ceramide translocation | GO:0099040 | 2 / 3 | 366× | 9.63e-6 | 5.06e-4 ✓ sig. |
| cranial nerve development | GO:0021545 | 2 / 4 | 275× | 1.92e-5 | 8.71e-4 ✓ sig. |
| neuron apoptotic process | GO:0051402 | 4 / 98 | 22.4× | 2.92e-5 | 1.20e-3 ✓ sig. |
| ERBB2-ERBB4 signaling pathway | GO:0038135 | 2 / 5 | 220× | 3.20e-5 | 1.28e-3 ✓ sig. |
| B cell lineage commitment | GO:0002326 | 2 / 5 | 220× | 3.20e-5 | 1.28e-3 ✓ sig. |
| T cell lineage commitment | GO:0002360 | 2 / 6 | 183× | 4.80e-5 | 1.74e-3 ✓ sig. |
| cellular response to epidermal growth factor stimulus | GO:0071364 | 3 / 47 | 35.1× | 8.45e-5 | 2.67e-3 ✓ sig. |
| ERBB2-EGFR signaling pathway | GO:0038134 | 2 / 8 | 137× | 8.94e-5 | 2.78e-3 ✓ sig. |
| cell population proliferation | GO:0008283 | 5 / 263 | 10.4× | 1.06e-4 | 3.16e-3 ✓ sig. |
| ERBB2-ERBB3 signaling pathway | GO:0038133 | 2 / 9 | 122× | 1.15e-4 | 3.35e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Gallbladder neoplasms | Soft tissue neoplasms | 0.077 | 2 | 2.53e-6 | 1.46e-5 ✓ sig. |
| amyotrophic lateral sclerosis type 19 | Soft tissue neoplasms | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| amyotrophic lateral sclerosis type 19 | Peritoneal disease | 0.100 | 1 | 5.84e-4 | 1.14e-3 ✓ sig. |
| Peritoneal disease | Soft tissue neoplasms | 0.091 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| amyotrophic lateral sclerosis type 19 | Gallbladder neoplasms | 0.038 | 1 | 1.62e-3 | 2.44e-3 ✓ sig. |
| Early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome | Gallbladder neoplasms | 0.038 | 1 | 1.62e-3 | 2.44e-3 ✓ sig. |
| Conjunctival disease | Gallbladder neoplasms | 0.037 | 1 | 3.24e-3 | 4.24e-3 ✓ sig. |