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.
← Back to all clusters
Cluster 399
6
Diseases
41
Unique genes
0.118
Avg. similarity score
Vertebral column disorder
Most-connected disease (4 links)
Disease
Searched: Abnormality of finger
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) ·
drag a node to pin it in place · scroll/pinch to zoom.
Abnormality of finger
Vertebral column disorder
Spondylosis
Abnormality of the thumb
Lamb-shaffer syndrome
Spastic tetraplegia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Vertebral column disorder | 4 | 4 | 13 |
| Spondylosis | 3 | 3 | 30 |
| Abnormality of finger | 2 | 2 | 1 |
| Abnormality of the thumb | 2 | 2 | 1 |
| Lamb-shaffer syndrome | 2 | 2 | 1 |
| Spastic tetraplegia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HEATR3 | 3 / 6 | Abnormality of finger, Abnormality of the thumb, Vertebral column disorder |
| SOX5 | 3 / 6 | Lamb-shaffer syndrome, Spondylosis, Vertebral column disorder |
| HLA-B | 2 / 6 | Spondylosis, Vertebral column disorder |
| KCNC2 | 2 / 6 | Spastic tetraplegia, Spondylosis |
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 ⇵ |
|---|---|---|---|---|---|
| Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | KEGG | 2 / 21 | 27.9× | 2.29e-3 | 2.11e-2 ✓ sig. |
| Glycosaminoglycan biosynthesis - heparan sulfate / heparin | KEGG | 2 / 24 | 24.4× | 2.99e-3 | 2.54e-2 ✓ sig. |
| TGF-beta signaling pathway | KEGG | 3 / 108 | 8.1× | 5.88e-3 | 4.06e-2 ✓ sig. |
| Endocytosis | KEGG | 4 / 250 | 4.7× | 1.01e-2 | 5.74e-2 |
| FGFR1c and Klotho ligand binding and activation | Reactome | 1 / 3 | 97.6× | 1.02e-2 | 5.76e-2 |
| SMAD4 MH2 Domain Mutants in Cancer | Reactome | 1 / 3 | 97.6× | 1.02e-2 | 5.76e-2 |
| SMAD2/3 MH2 Domain Mutants in Cancer | Reactome | 1 / 3 | 97.6× | 1.02e-2 | 5.76e-2 |
| Hippo signaling pathway | KEGG | 3 / 157 | 5.6× | 1.63e-2 | 7.60e-2 |
| RUNX3 regulates BCL2L11 (BIM) transcription | Reactome | 1 / 5 | 58.6× | 1.70e-2 | 7.80e-2 |
| Cell adhesion molecules | KEGG | 3 / 160 | 5.5× | 1.71e-2 | 7.84e-2 |
| Signaling by NODAL | Reactome | 1 / 6 | 48.8× | 2.03e-2 | 8.65e-2 |
| SMAD2/3 Phosphorylation Motif Mutants in Cancer | Reactome | 1 / 6 | 48.8× | 2.03e-2 | 8.65e-2 |
| TGFBR1 KD Mutants in Cancer | Reactome | 1 / 6 | 48.8× | 2.03e-2 | 8.65e-2 |
| RUNX3 regulates CDKN1A transcription | Reactome | 1 / 7 | 41.8× | 2.37e-2 | 9.45e-2 |
| 2-LTR circle formation | Reactome | 1 / 7 | 41.8× | 2.37e-2 | 9.45e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of chondrocyte differentiation | GO:0032332 | 3 / 20 | 68.4× | 1.09e-5 | 5.81e-4 ✓ sig. |
| positive regulation of bone mineralization | GO:0030501 | 3 / 42 | 32.6× | 1.06e-4 | 3.23e-3 ✓ sig. |
| response to angiotensin | GO:1990776 | 2 / 12 | 76.0× | 3.06e-4 | 6.87e-3 ✓ sig. |
| response to magnesium ion | GO:0032026 | 2 / 12 | 76.0× | 3.06e-4 | 6.87e-3 ✓ sig. |
| regulation of ARF protein signal transduction | GO:0032012 | 2 / 19 | 48.0× | 7.84e-4 | 1.27e-2 ✓ sig. |
| cartilage development | GO:0051216 | 3 / 89 | 15.4× | 9.77e-4 | 1.44e-2 ✓ sig. |
| chondroitin sulfate proteoglycan biosynthetic process | GO:0050650 | 2 / 26 | 35.1× | 1.48e-3 | 1.82e-2 ✓ sig. |
| heparan sulfate proteoglycan biosynthetic process | GO:0015012 | 2 / 30 | 30.4× | 1.97e-3 | 2.10e-2 ✓ sig. |
| establishment of integrated proviral latency | GO:0075713 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| mercury ion transport | GO:0015694 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| leukocyte adhesion to arterial endothelial cell | GO:0061757 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| plasma membrane selenite transport | GO:0097080 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| mitochondrial manganese ion transmembrane transport | GO:1990540 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| negative regulation of lung blood pressure | GO:0061767 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
| mitotic DNA integrity checkpoint signaling | GO:0044774 | 1 / 1 | 456× | 2.19e-3 | 2.23e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Abnormality of finger | Abnormality of the thumb | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Spondylosis | Vertebral column disorder | 0.048 | 2 | 2.79e-4 | 5.82e-4 ✓ sig. |
| Abnormality of finger | Vertebral column disorder | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Abnormality of the thumb | Vertebral column disorder | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Lamb-shaffer syndrome | Vertebral column disorder | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Lamb-shaffer syndrome | Spondylosis | 0.032 | 1 | 1.94e-3 | 2.65e-3 ✓ sig. |
| Spastic tetraplegia | Spondylosis | 0.032 | 1 | 1.94e-3 | 2.65e-3 ✓ sig. |