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 313
6
Diseases
7
Unique genes
0.244
Avg. similarity score
Antithrombin deficiency
Most-connected disease (4 links)
Disease
Searched: Craniocerebral trauma
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Craniocerebral trauma
Antithrombin deficiency
Bronchiolitis
Diffuse panbronchiolitis
Hereditary antithrombin deficiency
Interstitial systitis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Antithrombin deficiency | 4 | 4 | 3 |
| Bronchiolitis | 3 | 3 | 4 |
| Craniocerebral trauma | 2 | 2 | 1 |
| Diffuse panbronchiolitis | 2 | 2 | 2 |
| Hereditary antithrombin deficiency | 2 | 2 | 1 |
| Interstitial systitis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| MUC5B | 3 / 6 | Antithrombin deficiency, Bronchiolitis, Diffuse panbronchiolitis |
| SERPINC1 | 3 / 6 | Antithrombin deficiency, Craniocerebral trauma, Hereditary antithrombin deficiency |
| ADRB2 | 2 / 6 | Bronchiolitis, Interstitial systitis |
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 ⇵ |
|---|---|---|---|---|---|
| IL-17 signaling pathway | KEGG | 3 / 94 | 54.8× | 1.59e-5 | 5.01e-4 ✓ sig. |
| Inflammatory bowel disease | KEGG | 2 / 66 | 52.0× | 6.14e-4 | 9.54e-3 ✓ sig. |
| Salivary secretion | KEGG | 2 / 93 | 36.9× | 1.21e-3 | 1.61e-2 ✓ sig. |
| Rheumatoid arthritis | KEGG | 2 / 95 | 36.1× | 1.27e-3 | 1.66e-2 ✓ sig. |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 2 / 108 | 31.8× | 1.63e-3 | 2.01e-2 ✓ sig. |
| Th17 cell differentiation | KEGG | 2 / 109 | 31.5× | 1.66e-3 | 2.04e-2 ✓ sig. |
| Alcoholic liver disease | KEGG | 2 / 144 | 23.8× | 2.88e-3 | 3.04e-2 ✓ sig. |
| CLEC7A/inflammasome pathway | Reactome | 1 / 6 | 286× | 3.49e-3 | 3.48e-2 ✓ sig. |
| Interleukin-17 signaling | Reactome | 1 / 8 | 214× | 4.65e-3 | 4.24e-2 ✓ sig. |
| Interleukin-1 processing | Reactome | 1 / 8 | 214× | 4.65e-3 | 4.24e-2 ✓ sig. |
| Adrenoceptors | Reactome | 1 / 9 | 191× | 5.24e-3 | 4.60e-2 ✓ sig. |
| Defective GALNT3 causes familial hyperphosphatemic tumoral calcinosis (HFTC) | Reactome | 1 / 17 | 101× | 9.87e-3 | 6.95e-2 |
| Defective GALNT12 causes colorectal cancer 1 (CRCS1) | Reactome | 1 / 17 | 101× | 9.87e-3 | 6.95e-2 |
| Defective C1GALT1C1 causes Tn polyagglutination syndrome (TNPS) | Reactome | 1 / 18 | 95.3× | 1.04e-2 | 7.20e-2 |
| Cytokine-cytokine receptor interaction | KEGG | 2 / 298 | 11.5× | 1.19e-2 | 7.78e-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 interleukin-16 production | GO:0032739 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| regulation of systemic arterial blood pressure by norepinephrine-epinephrine | GO:0001993 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| positive regulation of mini excitatory postsynaptic potential | GO:0061885 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| positive regulation of interleukin-6 production | GO:0032755 | 2 / 103 | 51.8× | 6.21e-4 | 1.13e-2 ✓ sig. |
| negative regulation of gap junction assembly | GO:1903597 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| positive regulation of antimicrobial peptide production | GO:0002225 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| granulocyte migration | GO:0097530 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| positive regulation of tumor necrosis factor superfamily cytokine production | GO:1903557 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| positive regulation of complement activation | GO:0045917 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| regulation of nitric-oxide synthase activity | GO:0050999 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| positive regulation of RNA biosynthetic process | GO:1902680 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| defense response to Gram-positive bacterium | GO:0050830 | 2 / 135 | 39.5× | 1.06e-3 | 1.60e-2 ✓ sig. |
| norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure | GO:0002025 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| monocyte aggregation | GO:0070487 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| fever generation | GO:0001660 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Craniocerebral trauma | Hereditary antithrombin deficiency | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Antithrombin deficiency | Craniocerebral trauma | 0.250 | 1 | 1.95e-4 | 5.32e-4 ✓ sig. |
| Antithrombin deficiency | Hereditary antithrombin deficiency | 0.250 | 1 | 1.95e-4 | 5.32e-4 ✓ sig. |
| Bronchiolitis | Interstitial systitis | 0.200 | 1 | 2.60e-4 | 6.48e-4 ✓ sig. |
| Antithrombin deficiency | Diffuse panbronchiolitis | 0.200 | 1 | 3.90e-4 | 8.64e-4 ✓ sig. |
| Bronchiolitis | Diffuse panbronchiolitis | 0.167 | 1 | 5.19e-4 | 1.06e-3 ✓ sig. |
| Antithrombin deficiency | Bronchiolitis | 0.143 | 1 | 7.79e-4 | 1.40e-3 ✓ sig. |