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 496
6
Diseases
9
Unique genes
0.239
Avg. similarity score
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome
Most-connected disease (5 links)
Disease
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Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome
Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Hemimegalencephaly
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome | 5 | 5 | 3 |
| Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes | 4 | 4 | 3 |
| Hemimegalencephaly | 3 | 3 | 7 |
| Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 | 3 | 3 | 1 |
| Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 | 2 | 2 | 1 |
| Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AKT3 | 4 / 6 | Hemimegalencephaly, Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes |
| PIK3R2 | 3 / 6 | Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1, Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes |
| CCND2 | 2 / 6 | Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3 |
| MTOR | 2 / 6 | Hemimegalencephaly, Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes |
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 ⇵ |
|---|---|---|---|---|---|
| Cellular senescence | KEGG | 7 / 157 | 59.5× | 2.01e-12 | 3.56e-10 ✓ sig. |
| mTOR signaling pathway | KEGG | 7 / 158 | 59.1× | 2.10e-12 | 3.71e-10 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 8 / 361 | 29.6× | 5.41e-12 | 8.76e-10 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 6 / 80 | 100× | 5.97e-12 | 9.52e-10 ✓ sig. |
| Insulin signaling pathway | KEGG | 6 / 138 | 58.0× | 1.69e-10 | 1.86e-8 ✓ sig. |
| Human papillomavirus infection | KEGG | 7 / 333 | 28.1× | 4.06e-10 | 4.13e-8 ✓ sig. |
| Autophagy - animal | KEGG | 6 / 169 | 47.4× | 5.76e-10 | 5.67e-8 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 5 / 71 | 94.0× | 7.74e-10 | 7.37e-8 ✓ sig. |
| CD28 dependent PI3K/Akt signaling | Reactome | 4 / 22 | 243× | 1.06e-9 | 9.79e-8 ✓ sig. |
| Glioma | KEGG | 5 / 76 | 87.8× | 1.10e-9 | 1.01e-7 ✓ sig. |
| Longevity regulating pathway | KEGG | 5 / 90 | 74.1× | 2.60e-9 | 2.20e-7 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 5 / 90 | 74.1× | 2.60e-9 | 2.20e-7 ✓ sig. |
| Prostate cancer | KEGG | 5 / 98 | 68.1× | 4.01e-9 | 3.27e-7 ✓ sig. |
| Choline metabolism in cancer | KEGG | 5 / 99 | 67.4× | 4.22e-9 | 3.42e-7 ✓ sig. |
| Insulin resistance | KEGG | 5 / 109 | 61.2× | 6.87e-9 | 5.29e-7 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| insulin receptor signaling pathway | GO:0008286 | 4 / 80 | 104× | 3.86e-8 | 5.66e-6 ✓ sig. |
| phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0043491 | 4 / 92 | 90.3× | 6.80e-8 | 9.22e-6 ✓ sig. |
| positive regulation of TOR signaling | GO:0032008 | 3 / 36 | 173× | 5.47e-7 | 5.26e-5 ✓ sig. |
| negative regulation of cell size | GO:0045792 | 2 / 9 | 461× | 7.41e-6 | 4.32e-4 ✓ sig. |
| cellular response to insulin stimulus | GO:0032869 | 3 / 102 | 61.1× | 1.30e-5 | 6.65e-4 ✓ sig. |
| anoikis | GO:0043276 | 2 / 12 | 346× | 1.36e-5 | 6.89e-4 ✓ sig. |
| negative regulation of macroautophagy | GO:0016242 | 2 / 14 | 297× | 1.87e-5 | 8.78e-4 ✓ sig. |
| cytoplasmic translation | GO:0002181 | 3 / 126 | 49.4× | 2.44e-5 | 1.07e-3 ✓ sig. |
| TOR signaling | GO:0031929 | 2 / 24 | 173× | 5.66e-5 | 2.02e-3 ✓ sig. |
| positive regulation of oligodendrocyte differentiation | GO:0048714 | 2 / 25 | 166× | 6.15e-5 | 2.16e-3 ✓ sig. |
| negative regulation of cellular senescence | GO:2000773 | 2 / 26 | 160× | 6.66e-5 | 2.28e-3 ✓ sig. |
| regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0051896 | 2 / 27 | 154× | 7.19e-5 | 2.42e-3 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 4 / 532 | 15.6× | 7.30e-5 | 2.45e-3 ✓ sig. |
| positive regulation of lamellipodium assembly | GO:0010592 | 2 / 28 | 148× | 7.74e-5 | 2.56e-3 ✓ sig. |
| positive regulation of ubiquitin-dependent protein catabolic process | GO:2000060 | 2 / 30 | 138× | 8.91e-5 | 2.84e-3 ✓ sig. |