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 386
5
Diseases
83
Unique genes
0.149
Avg. similarity score
Hyperopia
Most-connected disease (4 links)
Disease
Searched: Congenital vertebral-cardiac-renal anomalies syndrome
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Congenital vertebral-cardiac-renal anomalies syndrome
Hyperopia
Catel-manzke syndrome
Vertebral, cardiac, renal, and limb defects syndrome
Trichotillomania
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Hyperopia | 4 | 4 | 79 |
| Catel-manzke syndrome | 3 | 3 | 2 |
| Congenital vertebral-cardiac-renal anomalies syndrome | 3 | 3 | 3 |
| Vertebral, cardiac, renal, and limb defects syndrome | 3 | 3 | 4 |
| Trichotillomania | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| KYNU | 4 / 5 | Catel-manzke syndrome, Congenital vertebral-cardiac-renal anomalies syndrome, Hyperopia, Vertebral, cardiac, renal, and limb defects syndrome |
| NADSYN1 | 3 / 5 | Congenital vertebral-cardiac-renal anomalies syndrome, Hyperopia, Vertebral, cardiac, renal, and limb defects syndrome |
| HAAO | 2 / 5 | Congenital vertebral-cardiac-renal anomalies syndrome, Vertebral, cardiac, renal, and limb defects syndrome |
| SLITRK1 | 2 / 5 | Hyperopia, Trichotillomania |
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 ⇵ |
|---|---|---|---|---|---|
| Tryptophan catabolism | Reactome | 2 / 11 | 26.3× | 2.49e-3 | 2.77e-2 ✓ sig. |
| Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) | Reactome | 1 / 1 | 145× | 6.91e-3 | 5.61e-2 |
| Nicotinamide salvaging | Reactome | 2 / 19 | 15.2× | 7.48e-3 | 5.89e-2 |
| FMO oxidises nucleophiles | Reactome | 1 / 3 | 48.2× | 2.06e-2 | 1.09e-1 |
| Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors | Reactome | 1 / 3 | 48.2× | 2.06e-2 | 1.09e-1 |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 36.2× | 2.74e-2 | 1.28e-1 |
| Methionine salvage pathway | Reactome | 1 / 4 | 36.2× | 2.74e-2 | 1.28e-1 |
| Anchoring of the basal body to the plasma membrane | Reactome | 3 / 98 | 4.4× | 3.03e-2 | 1.35e-1 |
| Retinoid metabolism and transport | Reactome | 2 / 41 | 7.1× | 3.25e-2 | 1.40e-1 |
| Tryptophan metabolism | KEGG | 2 / 42 | 6.9× | 3.40e-2 | 1.44e-1 |
| Electric Transmission Across Gap Junctions | Reactome | 1 / 5 | 28.9× | 3.41e-2 | 1.44e-1 |
| Chylomicron clearance | Reactome | 1 / 5 | 28.9× | 3.41e-2 | 1.44e-1 |
| Voltage gated Potassium channels | Reactome | 2 / 43 | 6.7× | 3.55e-2 | 1.47e-1 |
| Assembly and cell surface presentation of NMDA receptors | Reactome | 1 / 6 | 24.1× | 4.08e-2 | 1.58e-1 |
| Switching of origins to a post-replicative state | Reactome | 1 / 6 | 24.1× | 4.08e-2 | 1.58e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of neuronal synaptic plasticity | GO:0048168 | 4 / 26 | 34.6× | 5.02e-6 | 3.10e-4 ✓ sig. |
| 'de novo' NAD+ biosynthetic process from L-tryptophan | GO:0034354 | 3 / 9 | 75.0× | 6.96e-6 | 4.05e-4 ✓ sig. |
| NAD+ biosynthetic process | GO:0009435 | 3 / 13 | 52.0× | 2.34e-5 | 1.04e-3 ✓ sig. |
| anthranilate metabolic process | GO:0043420 | 2 / 3 | 150× | 5.83e-5 | 2.08e-3 ✓ sig. |
| quinolinate biosynthetic process | GO:0019805 | 2 / 4 | 113× | 1.16e-4 | 3.48e-3 ✓ sig. |
| clustering of voltage-gated sodium channels | GO:0045162 | 2 / 6 | 75.0× | 2.89e-4 | 6.77e-3 ✓ sig. |
| face morphogenesis | GO:0060325 | 3 / 33 | 20.5× | 4.19e-4 | 8.78e-3 ✓ sig. |
| cerebellar cortex development | GO:0021695 | 2 / 8 | 56.3× | 5.36e-4 | 1.03e-2 ✓ sig. |
| negative regulation of canonical Wnt signaling pathway | GO:0090090 | 5 / 150 | 7.5× | 5.47e-4 | 1.05e-2 ✓ sig. |
| L-tryptophan catabolic process | GO:0006569 | 2 / 9 | 50.0× | 6.88e-4 | 1.23e-2 ✓ sig. |
| head morphogenesis | GO:0060323 | 2 / 10 | 45.0× | 8.57e-4 | 1.41e-2 ✓ sig. |
| pyridine nucleotide biosynthetic process | GO:0019363 | 2 / 11 | 40.9× | 1.04e-3 | 1.61e-2 ✓ sig. |
| skeletal system morphogenesis | GO:0048705 | 3 / 45 | 15.0× | 1.05e-3 | 1.61e-2 ✓ sig. |
| excitatory chemical synaptic transmission | GO:0098976 | 2 / 13 | 34.6× | 1.47e-3 | 1.97e-2 ✓ sig. |
| visual perception | GO:0007601 | 5 / 215 | 5.2× | 2.70e-3 | 2.77e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital vertebral-cardiac-renal anomalies syndrome | Vertebral, cardiac, renal, and limb defects syndrome | 0.600 | 3 | 6.58e-12 | 7.30e-11 ✓ sig. |
| Congenital vertebral-cardiac-renal anomalies syndrome | Hyperopia | 0.025 | 2 | 7.77e-5 | 2.78e-4 ✓ sig. |
| Hyperopia | Vertebral, cardiac, renal, and limb defects syndrome | 0.024 | 2 | 1.55e-4 | 4.67e-4 ✓ sig. |
| Catel-manzke syndrome | Congenital vertebral-cardiac-renal anomalies syndrome | 0.200 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Catel-manzke syndrome | Vertebral, cardiac, renal, and limb defects syndrome | 0.167 | 1 | 5.19e-4 | 1.06e-3 ✓ sig. |
| Catel-manzke syndrome | Hyperopia | 0.012 | 1 | 1.02e-2 | 1.16e-2 ✓ sig. |
| Hyperopia | Trichotillomania | 0.012 | 1 | 1.02e-2 | 1.16e-2 ✓ sig. |