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 497
6
Diseases
2
Unique genes
0.444
Avg. similarity score
Cutis marmorata
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Cutis marmorata
Evans syndrome
Immune deficiency, autoimmune disease and intellectual disability
Immunodeficiency 78 with autoimmunity and developmental delay
Tpp2 deficiency
White matter abnormalities
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cutis marmorata | 5 | 5 | 1 |
| Evans syndrome | 5 | 5 | 1 |
| Immune deficiency, autoimmune disease and intellectual disability | 5 | 5 | 1 |
| Immunodeficiency 78 with autoimmunity and developmental delay | 5 | 5 | 1 |
| Tpp2 deficiency | 5 | 5 | 1 |
| White matter abnormalities | 5 | 5 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TPP2 | 6 / 6 | Cutis marmorata, Evans syndrome, Immune deficiency, autoimmune disease and intellectual disability, Immunodeficiency 78 with autoimmunity and developmental delay and 2 more |
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 ⇵ |
|---|---|---|---|---|---|
| Pink/Parkin Mediated Mitophagy | Reactome | 1 / 22 | 273× | 3.66e-3 | 2.93e-2 ✓ sig. |
| Mitophagy - animal | KEGG | 1 / 105 | 57.2× | 1.74e-2 | 7.89e-2 |
| Ub-specific processing proteases | Reactome | 1 / 220 | 27.3× | 3.63e-2 | 1.20e-1 |
| Antigen processing: Ubiquitination & Proteasome degradation | Reactome | 1 / 309 | 19.4× | 5.08e-2 | 1.46e-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 ⇵ |
|---|---|---|---|---|---|
| response to thyroxine | GO:0097068 | 1 / 3 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| intracellular amino acid homeostasis | GO:0080144 | 1 / 3 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| protein insertion into mitochondrial outer membrane | GO:0045040 | 1 / 12 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| mRNA transcription | GO:0009299 | 1 / 13 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| protein insertion into mitochondrial inner membrane | GO:0045039 | 1 / 13 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| negative regulation of cell growth involved in cardiac muscle cell development | GO:0061052 | 1 / 14 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| protein import into mitochondrial matrix | GO:0030150 | 1 / 24 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| protein targeting to mitochondrion | GO:0006626 | 1 / 29 | 322× | 3.10e-3 | 2.65e-2 ✓ sig. |
| positive regulation of defense response to virus by host | GO:0002230 | 1 / 32 | 292× | 3.42e-3 | 2.78e-2 ✓ sig. |
| positive regulation of protein targeting to mitochondrion | GO:1903955 | 1 / 33 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| activation of innate immune response | GO:0002218 | 1 / 37 | 253× | 3.96e-3 | 3.00e-2 ✓ sig. |
| positive regulation of interferon-beta production | GO:0032728 | 1 / 41 | 228× | 4.38e-3 | 3.14e-2 ✓ sig. |
| antiviral innate immune response | GO:0140374 | 1 / 79 | 118× | 8.44e-3 | 4.30e-2 ✓ sig. |
| cellular response to virus | GO:0098586 | 1 / 89 | 105× | 9.50e-3 | 4.55e-2 ✓ sig. |
| protein polyubiquitination | GO:0000209 | 1 / 153 | 61.1× | 1.63e-2 | 5.91e-2 |