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 590
5
Diseases
13
Unique genes
0.071
Avg. similarity score
Brain atrophy
Most-connected disease (4 links)
Disease
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Brain atrophy
Neurodegeneration, childhood-onset, with progressive microcephaly
Neurodevelopmental disorder with seizures and brain atrophy
Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities
Optic atrophy 9
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Brain atrophy | 4 | 4 | 13 |
| Neurodegeneration, childhood-onset, with progressive microcephaly | 1 | 1 | 1 |
| Neurodevelopmental disorder with seizures and brain atrophy | 1 | 1 | 1 |
| Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities | 1 | 1 | 1 |
| Optic atrophy 9 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ACO2 | 2 / 5 | Brain atrophy, Optic atrophy 9 |
| DTYMK | 2 / 5 | Brain atrophy, Neurodegeneration, childhood-onset, with progressive microcephaly |
| EXOC7 | 2 / 5 | Brain atrophy, Neurodevelopmental disorder with seizures and brain atrophy |
| GRM7 | 2 / 5 | Brain atrophy, Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities |
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 ⇵ |
|---|---|---|---|---|---|
| PTK6 promotes HIF1A stabilization | Reactome | 1 / 6 | 154× | 6.48e-3 | 4.32e-2 ✓ sig. |
| Lysosome | KEGG | 2 / 133 | 13.9× | 8.76e-3 | 5.24e-2 |
| Negative regulation of activity of TFAP2 (AP-2) family transcription factors | Reactome | 1 / 9 | 103× | 9.70e-3 | 5.59e-2 |
| RHO GTPases activate KTN1 | Reactome | 1 / 11 | 84.0× | 1.18e-2 | 6.31e-2 |
| Activation of the TFAP2 (AP-2) family of transcription factors | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 6.62e-2 |
| Insulin processing | Reactome | 1 / 14 | 66.0× | 1.51e-2 | 7.27e-2 |
| LDL clearance | Reactome | 1 / 18 | 51.3× | 1.93e-2 | 8.40e-2 |
| Interleukin-37 signaling | Reactome | 1 / 21 | 44.0× | 2.25e-2 | 9.16e-2 |
| VxPx cargo-targeting to cilium | Reactome | 1 / 21 | 44.0× | 2.25e-2 | 9.16e-2 |
| Citric acid cycle (TCA cycle) | Reactome | 1 / 22 | 42.0× | 2.36e-2 | 9.42e-2 |
| Nuclear signaling by ERBB4 | Reactome | 1 / 24 | 38.5× | 2.57e-2 | 9.90e-2 |
| Salmonella infection | KEGG | 2 / 248 | 7.5× | 2.85e-2 | 1.05e-1 |
| Interconversion of nucleotide di- and triphosphates | Reactome | 1 / 29 | 31.9× | 3.10e-2 | 1.10e-1 |
| Citrate cycle (TCA cycle) | KEGG | 1 / 30 | 30.8× | 3.20e-2 | 1.12e-1 |
| Glyoxylate and dicarboxylate metabolism | KEGG | 1 / 30 | 30.8× | 3.20e-2 | 1.12e-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 ⇵ |
|---|---|---|---|---|---|
| protein transmembrane transport | GO:0071806 | 2 / 19 | 151× | 7.59e-5 | 2.52e-3 ✓ sig. |
| regulation of synaptic transmission, glutamatergic | GO:0051966 | 2 / 33 | 87.1× | 2.33e-4 | 5.65e-3 ✓ sig. |
| cellular response to curcumin | GO:1904644 | 1 / 1 | 1,437× | 6.96e-4 | 1.18e-2 ✓ sig. |
| Wnt signalosome assembly | GO:1904887 | 1 / 1 | 1,437× | 6.96e-4 | 1.18e-2 ✓ sig. |
| regulation of isoprenoid metabolic process | GO:0019747 | 1 / 1 | 1,437× | 6.96e-4 | 1.18e-2 ✓ sig. |
| positive regulation of homophilic cell adhesion | GO:1903387 | 1 / 1 | 1,437× | 6.96e-4 | 1.18e-2 ✓ sig. |
| regulation of kidney size | GO:0035564 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| negative regulation of late endosome to lysosome transport | GO:1902823 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| negative regulation of protein processing involved in protein targeting to mitochondrion | GO:1903217 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| positive regulation of adherens junction organization | GO:1903393 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| regulation of modification of synapse structure, modulating synaptic transmission | GO:0098987 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| dUDP biosynthetic process | GO:0006227 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| dTDP biosynthetic process | GO:0006233 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| regulation of membrane potential | GO:0042391 | 2 / 85 | 33.8× | 1.54e-3 | 1.86e-2 ✓ sig. |
| protein localization to basolateral plasma membrane | GO:1903361 | 1 / 3 | 479× | 2.09e-3 | 2.17e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Brain atrophy | Optic atrophy 9 | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Brain atrophy | Neurodegeneration, childhood-onset, with progressive microcephaly | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Brain atrophy | Neurodevelopmental disorder with seizures and brain atrophy | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Brain atrophy | Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |