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 441
6
Diseases
7
Unique genes
0.266
Avg. similarity score
Ataxia, spastic, autosomal recessive
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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Ataxia, spastic, autosomal recessive
Ataxia and seizures
Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome
Optic atrophy and/or spastic ataxia spectrum
Spastic ataxia optic atrophy dysarthria syndrome
Spastic ataxia with leukoencephalopathy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ataxia, spastic, autosomal recessive | 5 | 5 | 7 |
| Ataxia and seizures | 3 | 3 | 1 |
| Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome | 3 | 3 | 1 |
| Optic atrophy and/or spastic ataxia spectrum | 3 | 3 | 1 |
| Spastic ataxia optic atrophy dysarthria syndrome | 1 | 1 | 1 |
| Spastic ataxia with leukoencephalopathy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AFG3L2 | 4 / 6 | Ataxia and seizures, Ataxia, spastic, autosomal recessive, Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome, Optic atrophy and/or spastic ataxia spectrum |
| MARS2 | 2 / 6 | Ataxia, spastic, autosomal recessive, Spastic ataxia with leukoencephalopathy |
| MTPAP | 2 / 6 | Ataxia, spastic, autosomal recessive, Spastic ataxia optic atrophy dysarthria syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Ubiquinone and other terpenoid-quinone biosynthesis | KEGG | 1 / 12 | 143× | 6.97e-3 | 4.53e-2 ✓ sig. |
| Hyaluronan uptake and degradation | Reactome | 1 / 12 | 143× | 6.97e-3 | 4.53e-2 ✓ sig. |
| Mitochondrial tRNA aminoacylation | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| Processing of SMDT1 | Reactome | 1 / 16 | 107× | 9.29e-3 | 5.43e-2 |
| Selenocompound metabolism | KEGG | 1 / 17 | 101× | 9.87e-3 | 5.65e-2 |
| Kinesins | Reactome | 1 / 59 | 29.1× | 3.39e-2 | 1.16e-1 |
| Aminoacyl-tRNA biosynthesis | KEGG | 1 / 66 | 26.0× | 3.78e-2 | 1.23e-1 |
| COPI-dependent Golgi-to-ER retrograde traffic | Reactome | 1 / 99 | 17.3× | 5.63e-2 | 1.55e-1 |
| Spinocerebellar ataxia | KEGG | 1 / 144 | 11.9× | 8.10e-2 | 1.91e-1 |
| Biosynthesis of cofactors | KEGG | 1 / 154 | 11.1× | 8.64e-2 | 1.98e-1 |
| Motor proteins | KEGG | 1 / 194 | 8.8× | 1.08e-1 | 2.26e-1 |
| Metabolic pathways | KEGG | 2 / 1,563 | 2.2× | 2.29e-1 | 3.61e-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 ⇵ |
|---|---|---|---|---|---|
| membrane docking | GO:0022406 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| positive regulation of protein transport | GO:0051222 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| cellular response to glutathione | GO:0072753 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| glutathione import into mitochondrion | GO:0160007 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| methionyl-tRNA aminoacylation | GO:0006431 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| positive regulation of sodium:proton antiporter activity | GO:0032417 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| mitochondrial RNA 3'-end processing | GO:0000965 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| regulation of calcium import into the mitochondrion | GO:0110097 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| negative regulation of phosphatase activity | GO:0010923 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| negative regulation of cell fate commitment | GO:0010454 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| positive regulation of protein glycosylation | GO:0060050 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| anterograde neuronal dense core vesicle transport | GO:1990048 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| negative regulation of protein autophosphorylation | GO:0031953 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| mitochondrial mRNA polyadenylation | GO:0097222 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| mitochondrial protein quality control | GO:0141164 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Ataxia and seizures | Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Ataxia and seizures | Optic atrophy and/or spastic ataxia spectrum | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome | Optic atrophy and/or spastic ataxia spectrum | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Ataxia and seizures | Ataxia, spastic, autosomal recessive | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Ataxia, spastic, autosomal recessive | Spastic ataxia with leukoencephalopathy | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Ataxia, spastic, autosomal recessive | Early-onset spastic ataxia-myoclonic epilepsy-neuropathy syndrome | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Ataxia, spastic, autosomal recessive | Optic atrophy and/or spastic ataxia spectrum | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |
| Ataxia, spastic, autosomal recessive | Spastic ataxia optic atrophy dysarthria syndrome | 0.125 | 1 | 4.52e-4 | 8.26e-4 ✓ sig. |