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 318
7
Diseases
7
Unique genes
0.258
Avg. similarity score
Muscular hypotonia
Most-connected disease (5 links)
Disease
Searched: Abnormality of the eye
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Abnormality of the eye
Muscular hypotonia
Central hypotonia
Hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities
Hypoventilation
Basilicata-akhtar syndrome
Intellectual developmental disorder peripheral neuropathy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Muscular hypotonia | 5 | 5 | 4 |
| Central hypotonia | 4 | 4 | 2 |
| Hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities | 4 | 4 | 1 |
| Hypoventilation | 4 | 4 | 1 |
| Abnormality of the eye | 3 | 3 | 3 |
| Basilicata-akhtar syndrome | 1 | 1 | 1 |
| Intellectual developmental disorder peripheral neuropathy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| P4HTM | 5 / 7 | Abnormality of the eye, Central hypotonia, Hypotonia, hypoventilation, impaired intellectual development, dysautonomia, epilepsy, and eye abnormalities, Hypoventilation and 1 more |
| MSL3 | 2 / 7 | Basilicata-akhtar syndrome, Muscular hypotonia |
| NUDT2 | 2 / 7 | Intellectual developmental disorder peripheral neuropathy, Muscular hypotonia |
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 ⇵ |
|---|---|---|---|---|---|
| Inhibition of replication initiation of damaged DNA by RB1/E2F1 | Reactome | 1 / 10 | 172× | 5.82e-3 | 4.03e-2 ✓ sig. |
| ERKs are inactivated | Reactome | 1 / 13 | 132× | 7.55e-3 | 4.77e-2 ✓ sig. |
| APC truncation mutants have impaired AXIN binding | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| AXIN missense mutants destabilize the destruction complex | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| Truncations of AMER1 destabilize the destruction complex | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| ERK/MAPK targets | Reactome | 1 / 14 | 123× | 8.13e-3 | 5.01e-2 |
| Misspliced GSK3beta mutants stabilize beta-catenin | Reactome | 1 / 15 | 114× | 8.71e-3 | 5.22e-2 |
| S33 mutants of beta-catenin aren't phosphorylated | Reactome | 1 / 15 | 114× | 8.71e-3 | 5.22e-2 |
| S37 mutants of beta-catenin aren't phosphorylated | Reactome | 1 / 15 | 114× | 8.71e-3 | 5.22e-2 |
| S45 mutants of beta-catenin aren't phosphorylated | Reactome | 1 / 15 | 114× | 8.71e-3 | 5.22e-2 |
| T41 mutants of beta-catenin aren't phosphorylated | Reactome | 1 / 15 | 114× | 8.71e-3 | 5.22e-2 |
| Spry regulation of FGF signaling | Reactome | 1 / 16 | 107× | 9.29e-3 | 5.43e-2 |
| Beta-catenin phosphorylation cascade | Reactome | 1 / 17 | 101× | 9.87e-3 | 5.65e-2 |
| Platelet sensitization by LDL | Reactome | 1 / 17 | 101× | 9.87e-3 | 5.65e-2 |
| DARPP-32 events | Reactome | 1 / 19 | 90.3× | 1.10e-2 | 6.03e-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 ⇵ |
|---|---|---|---|---|---|
| AMP biosynthetic process | GO:0006167 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| negative regulation of glycolytic process through fructose-6-phosphate | GO:1904539 | 1 / 4 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| vascular endothelial cell response to oscillatory fluid shear stress | GO:0097706 | 1 / 5 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| regulation of erythrocyte differentiation | GO:0045646 | 1 / 6 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| positive regulation of focal adhesion disassembly | GO:0120183 | 1 / 8 | 334× | 2.99e-3 | 2.59e-2 ✓ sig. |
| peptidyl-threonine dephosphorylation | GO:0035970 | 1 / 9 | 297× | 3.37e-3 | 2.76e-2 ✓ sig. |
| positive regulation of keratinocyte migration | GO:0051549 | 1 / 12 | 222× | 4.49e-3 | 3.17e-2 ✓ sig. |
| dendritic spine development | GO:0060996 | 1 / 15 | 178× | 5.61e-3 | 3.51e-2 ✓ sig. |
| regulation of microtubule polymerization | GO:0031113 | 1 / 16 | 167× | 5.98e-3 | 3.62e-2 ✓ sig. |
| response to lead ion | GO:0010288 | 1 / 17 | 157× | 6.35e-3 | 3.73e-2 ✓ sig. |
| regulation of ARF protein signal transduction | GO:0032012 | 1 / 19 | 141× | 7.10e-3 | 3.94e-2 ✓ sig. |
| RNA polymerase II transcription initiation surveillance | GO:0160240 | 1 / 20 | 133× | 7.47e-3 | 4.04e-2 ✓ sig. |
| regulation of growth | GO:0040008 | 1 / 23 | 116× | 8.59e-3 | 4.32e-2 ✓ sig. |
| negative regulation of hippo signaling | GO:0035331 | 1 / 25 | 107× | 9.33e-3 | 4.50e-2 ✓ sig. |
| ATP biosynthetic process | GO:0006754 | 1 / 26 | 103× | 9.70e-3 | 4.58e-2 ✓ sig. |