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 484
6
Diseases
6
Unique genes
0.381
Avg. similarity score
Charcot-Marie-Tooth disease axonal type 2N
Most-connected disease (5 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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Charcot-Marie-Tooth disease axonal type 2N
Developmental and epileptic encephalopathy, 29
Early-onset epileptic encephalopathy with persistent myelination defect
Leukoencephalopathy
Leukoencephalopathy, hereditary diffuse, with spheroids 2
Trichothiodystrophy 8, non-photosensitive
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Charcot-Marie-Tooth disease axonal type 2N | 5 | 5 | 1 |
| Developmental and epileptic encephalopathy, 29 | 5 | 5 | 1 |
| Early-onset epileptic encephalopathy with persistent myelination defect | 5 | 5 | 1 |
| Leukoencephalopathy | 5 | 5 | 6 |
| Leukoencephalopathy, hereditary diffuse, with spheroids 2 | 5 | 5 | 1 |
| Trichothiodystrophy 8, non-photosensitive | 5 | 5 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AARS1 | 6 / 6 | Charcot-Marie-Tooth disease axonal type 2N, Developmental and epileptic encephalopathy, 29, Early-onset epileptic encephalopathy with persistent myelination defect, Leukoencephalopathy 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 ⇵ |
|---|---|---|---|---|---|
| Resolution of AP sites via the single-nucleotide replacement pathway | Reactome | 1 / 3 | 667× | 1.50e-3 | 1.54e-2 ✓ sig. |
| APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway | Reactome | 1 / 7 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| Advanced glycosylation endproduct receptor signaling | Reactome | 1 / 8 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| Formyl peptide receptors bind formyl peptides and many other ligands | Reactome | 1 / 8 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| HDR through MMEJ (alt-NHEJ) | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Synthesis of PIPs at the late endosome membrane | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Pyrimidine salvage | Reactome | 1 / 11 | 182× | 5.48e-3 | 3.87e-2 ✓ sig. |
| Pyrimidine catabolism | Reactome | 1 / 11 | 182× | 5.48e-3 | 3.87e-2 ✓ sig. |
| Heme biosynthesis | Reactome | 1 / 14 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| The NLRP3 inflammasome | Reactome | 1 / 15 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Synthesis of PIPs at the early endosome membrane | Reactome | 1 / 15 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models | Reactome | 1 / 16 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Insertion of tail-anchored proteins into the endoplasmic reticulum membrane | Reactome | 1 / 16 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 1 / 18 | 111× | 8.96e-3 | 5.31e-2 |
| Cytosolic tRNA aminoacylation | Reactome | 1 / 24 | 83.4× | 1.19e-2 | 6.32e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of cytoplasmic translational fidelity | GO:0140018 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| positive regulation of Toll signaling pathway | GO:0045752 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| regulation of response to calcium ion | GO:1905945 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| negative regulation of mitochondrial DNA replication | GO:0090298 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| locomotory behavior | GO:0007626 | 2 / 99 | 62.9× | 4.11e-4 | 8.34e-3 ✓ sig. |
| protein trimerization | GO:0070206 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway | GO:1903381 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of blood circulation | GO:1903523 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| positive regulation of protein import | GO:1904591 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| pyrimidine nucleobase metabolic process | GO:0006206 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| pyrimidine-containing compound metabolic process | GO:0072527 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| alanyl-tRNA aminoacylation | GO:0006419 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| regulation of amyloid-beta clearance | GO:1900221 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| regulation of amyloid fibril formation | GO:1905906 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| phospholipase D-activating G protein-coupled receptor signaling pathway | GO:0031583 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |