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 360
5
Diseases
32
Unique genes
0.149
Avg. similarity score
Spondylosis
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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Spondylosis
Dna ligase iv deficiency
Dubowitz syndrome
Lig4 syndrome
Intellectual developmental disorder short stature behavioral
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Spondylosis | 4 | 4 | 30 |
| Dna ligase iv deficiency | 3 | 3 | 1 |
| Dubowitz syndrome | 3 | 3 | 2 |
| Lig4 syndrome | 3 | 3 | 2 |
| Intellectual developmental disorder short stature behavioral | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LIG4 | 4 / 5 | Dna ligase iv deficiency, Dubowitz syndrome, Lig4 syndrome, Spondylosis |
| IQSEC1 | 2 / 5 | Intellectual developmental disorder short stature behavioral, 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 ⇵ |
|---|---|---|---|---|---|
| 2-LTR circle formation | Reactome | 2 / 7 | 107× | 1.43e-4 | 3.00e-3 ✓ sig. |
| Non-homologous end-joining | KEGG | 2 / 13 | 57.7× | 5.27e-4 | 8.28e-3 ✓ sig. |
| Glycosaminoglycan biosynthesis - heparan sulfate / heparin | KEGG | 2 / 24 | 31.3× | 1.83e-3 | 2.14e-2 ✓ sig. |
| FGFR1c and Klotho ligand binding and activation | Reactome | 1 / 3 | 125× | 7.97e-3 | 5.96e-2 |
| Cell adhesion molecules | KEGG | 3 / 160 | 7.0× | 8.67e-3 | 6.30e-2 |
| Nonhomologous End-Joining (NHEJ) | Reactome | 2 / 69 | 10.9× | 1.44e-2 | 8.52e-2 |
| Sema4D mediated inhibition of cell attachment and migration | Reactome | 1 / 8 | 46.9× | 2.11e-2 | 1.06e-1 |
| Endosomal/Vacuolar pathway | Reactome | 1 / 8 | 46.9× | 2.11e-2 | 1.06e-1 |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 41.7× | 2.37e-2 | 1.13e-1 |
| Endocytosis | KEGG | 3 / 250 | 4.5× | 2.83e-2 | 1.25e-1 |
| The activation of arylsulfatases | Reactome | 1 / 13 | 28.9× | 3.41e-2 | 1.39e-1 |
| PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases | Reactome | 1 / 14 | 26.8× | 3.67e-2 | 1.44e-1 |
| Phospholipase C-mediated cascade: FGFR1 | Reactome | 1 / 16 | 23.5× | 4.18e-2 | 1.55e-1 |
| Downstream signaling of activated FGFR1 | Reactome | 1 / 18 | 20.9× | 4.69e-2 | 1.65e-1 |
| tRNA modification in the nucleus and cytosol | Reactome | 1 / 19 | 19.8× | 4.95e-2 | 1.71e-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 ⇵ |
|---|---|---|---|---|---|
| immunoglobulin V(D)J recombination | GO:0033152 | 2 / 6 | 195× | 4.24e-5 | 1.59e-3 ✓ sig. |
| double-strand break repair via nonhomologous end joining | GO:0006303 | 3 / 45 | 38.9× | 6.16e-5 | 2.10e-3 ✓ sig. |
| response to magnesium ion | GO:0032026 | 2 / 12 | 97.3× | 1.86e-4 | 4.79e-3 ✓ sig. |
| cellular response to lithium ion | GO:0071285 | 2 / 15 | 77.9× | 2.94e-4 | 6.62e-3 ✓ sig. |
| regulation of ARF protein signal transduction | GO:0032012 | 2 / 19 | 61.5× | 4.77e-4 | 9.29e-3 ✓ sig. |
| response to X-ray | GO:0010165 | 2 / 19 | 61.5× | 4.77e-4 | 9.29e-3 ✓ sig. |
| positive regulation of chondrocyte differentiation | GO:0032332 | 2 / 20 | 58.4× | 5.29e-4 | 9.96e-3 ✓ sig. |
| heparan sulfate proteoglycan biosynthetic process | GO:0015012 | 2 / 30 | 38.9× | 1.20e-3 | 1.69e-2 ✓ sig. |
| establishment of integrated proviral latency | GO:0075713 | 1 / 1 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| meiotic cell cycle checkpoint signaling | GO:0033313 | 1 / 1 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| mitotic DNA integrity checkpoint signaling | GO:0044774 | 1 / 1 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| negative regulation of chromosome organization | GO:2001251 | 1 / 1 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| base-excision repair | GO:0006284 | 2 / 37 | 31.6× | 1.82e-3 | 2.15e-2 ✓ sig. |
| positive regulation of bone mineralization | GO:0030501 | 2 / 42 | 27.8× | 2.34e-3 | 2.48e-2 ✓ sig. |
| mechanosensory behavior | GO:0007638 | 1 / 2 | 292× | 3.42e-3 | 3.03e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Dna ligase iv deficiency | Dubowitz syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Dna ligase iv deficiency | Lig4 syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Dubowitz syndrome | Lig4 syndrome | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Dna ligase iv deficiency | Spondylosis | 0.032 | 1 | 1.95e-3 | 2.81e-3 ✓ sig. |
| Intellectual developmental disorder short stature behavioral | Spondylosis | 0.032 | 1 | 1.95e-3 | 2.81e-3 ✓ sig. |
| Dubowitz syndrome | Spondylosis | 0.031 | 1 | 3.89e-3 | 4.94e-3 ✓ sig. |
| Lig4 syndrome | Spondylosis | 0.031 | 1 | 3.89e-3 | 4.94e-3 ✓ sig. |