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 535
5
Diseases
4
Unique genes
0.350
Avg. similarity score
Carasil syndrome
Most-connected disease (4 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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Carasil syndrome
Cerebral microangiopathy
Cognitive impairment
Degenerative disc disease
Psychiatric disturbance
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Carasil syndrome | 4 | 4 | 1 |
| Cerebral microangiopathy | 4 | 4 | 4 |
| Cognitive impairment | 4 | 4 | 2 |
| Degenerative disc disease | 4 | 4 | 1 |
| Psychiatric disturbance | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HTRA1 | 5 / 5 | Carasil syndrome, Cerebral microangiopathy, Cognitive impairment, Degenerative disc disease and 1 more |
| COL4A1 | 2 / 5 | Cerebral microangiopathy, Cognitive impairment |
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 ⇵ |
|---|---|---|---|---|---|
| Extracellular matrix organization | Reactome | 1 / 15 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Anchoring fibril formation | Reactome | 1 / 15 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Crosslinking of collagen fibrils | Reactome | 1 / 18 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| NCAM1 interactions | Reactome | 1 / 21 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| Non-integrin membrane-ECM interactions | Reactome | 1 / 24 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Laminin interactions | Reactome | 1 / 28 | 107× | 9.29e-3 | 5.43e-2 |
| Signaling by PDGF | Reactome | 1 / 33 | 91.0× | 1.09e-2 | 6.01e-2 |
| Collagen chain trimerization | Reactome | 1 / 44 | 68.2× | 1.46e-2 | 7.13e-2 |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 1 / 51 | 58.9× | 1.69e-2 | 7.78e-2 |
| Collagen degradation | Reactome | 1 / 52 | 57.7× | 1.72e-2 | 7.87e-2 |
| Collagen biosynthesis and modifying enzymes | Reactome | 1 / 67 | 44.8× | 2.21e-2 | 9.09e-2 |
| Degradation of the extracellular matrix | Reactome | 1 / 70 | 42.9× | 2.31e-2 | 9.31e-2 |
| Integrin cell surface interactions | Reactome | 1 / 81 | 37.1× | 2.67e-2 | 1.01e-1 |
| ECM-receptor interaction | KEGG | 1 / 89 | 33.7× | 2.93e-2 | 1.07e-1 |
| Small cell lung cancer | KEGG | 1 / 93 | 32.3× | 3.06e-2 | 1.10e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| renal tubule morphogenesis | GO:0061333 | 1 / 4 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| retinal blood vessel morphogenesis | GO:0061304 | 1 / 6 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| chorionic trophoblast cell differentiation | GO:0060718 | 1 / 6 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| collagen-activated tyrosine kinase receptor signaling pathway | GO:0038063 | 1 / 12 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| basement membrane organization | GO:0071711 | 1 / 29 | 161× | 6.19e-3 | 3.70e-2 ✓ sig. |
| negative regulation of osteoclast differentiation | GO:0045671 | 1 / 30 | 156× | 6.41e-3 | 3.73e-2 ✓ sig. |
| branching involved in blood vessel morphogenesis | GO:0001569 | 1 / 33 | 142× | 7.05e-3 | 3.93e-2 ✓ sig. |
| blood vessel morphogenesis | GO:0048514 | 1 / 34 | 137× | 7.26e-3 | 3.99e-2 ✓ sig. |
| neuromuscular junction development | GO:0007528 | 1 / 35 | 133× | 7.47e-3 | 4.04e-2 ✓ sig. |
| regulation of cytosolic calcium ion concentration | GO:0051480 | 1 / 39 | 120× | 8.32e-3 | 4.25e-2 ✓ sig. |
| programmed cell death | GO:0012501 | 1 / 42 | 111× | 8.96e-3 | 4.41e-2 ✓ sig. |
| placenta development | GO:0001890 | 1 / 48 | 97.3× | 1.02e-2 | 4.69e-2 ✓ sig. |
| cellular response to amino acid stimulus | GO:0071230 | 1 / 64 | 73.0× | 1.36e-2 | 5.40e-2 |
| negative regulation of BMP signaling pathway | GO:0030514 | 1 / 75 | 62.3× | 1.60e-2 | 5.84e-2 |
| epithelial cell differentiation | GO:0030855 | 1 / 110 | 42.5× | 2.33e-2 | 7.08e-2 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cerebral microangiopathy | Cognitive impairment | 0.400 | 2 | 5.00e-8 | 3.63e-7 ✓ sig. |
| Carasil syndrome | Psychiatric disturbance | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Carasil syndrome | Degenerative disc disease | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Degenerative disc disease | Psychiatric disturbance | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Carasil syndrome | Cognitive impairment | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Cognitive impairment | Degenerative disc disease | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Cognitive impairment | Psychiatric disturbance | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Carasil syndrome | Cerebral microangiopathy | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Cerebral microangiopathy | Degenerative disc disease | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Cerebral microangiopathy | Psychiatric disturbance | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |