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 175
9
Diseases
22
Unique genes
0.115
Avg. similarity score
Ear, patella, short stature syndrome
Most-connected disease (8 links)
Disease
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Ear, patella, short stature syndrome
Meier-gorlin syndrome
Dna replication fork stabilization factor donson-related microcephaly, short stature, limb abnormalities spectrum
Dwarfism
meier-gorlin syndrome 2
meier-gorlin syndrome 3
meier-gorlin syndrome 4
meier-gorlin syndrome 5
meier-gorlin syndrome 6
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ear, patella, short stature syndrome | 8 | 8 | 12 |
| Meier-gorlin syndrome | 8 | 8 | 11 |
| Dna replication fork stabilization factor donson-related microcephaly, short stature, limb abnormalities spectrum | 3 | 3 | 1 |
| Dwarfism | 3 | 3 | 10 |
| meier-gorlin syndrome 2 | 2 | 2 | 1 |
| meier-gorlin syndrome 3 | 2 | 2 | 1 |
| meier-gorlin syndrome 4 | 2 | 2 | 1 |
| meier-gorlin syndrome 5 | 2 | 2 | 1 |
| meier-gorlin syndrome 6 | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DONSON | 4 / 9 | Dna replication fork stabilization factor donson-related microcephaly, short stature, limb abnormalities spectrum, Dwarfism, Ear, patella, short stature syndrome, Meier-gorlin syndrome |
| CDC6 | 3 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome, meier-gorlin syndrome 5 |
| CDT1 | 3 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome, meier-gorlin syndrome 4 |
| GMNN | 3 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome, meier-gorlin syndrome 6 |
| ORC1 | 3 / 9 | Dwarfism, Ear, patella, short stature syndrome, Meier-gorlin syndrome |
| ORC4 | 3 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome, meier-gorlin syndrome 2 |
| ORC6 | 3 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome, meier-gorlin syndrome 3 |
| CDC45 | 2 / 9 | Ear, patella, short stature syndrome, Meier-gorlin syndrome |
| GINS3 | 2 / 9 | Ear, patella, short stature syndrome, Meier-gorlin 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 ⇵ |
|---|---|---|---|---|---|
| Activation of the pre-replicative complex | Reactome | 10 / 33 | 165× | 3.42e-21 | 3.37e-18 ✓ sig. |
| Assembly of the pre-replicative complex | Reactome | 8 / 15 | 291× | 1.91e-19 | 1.40e-16 ✓ sig. |
| Activation of ATR in response to replication stress | Reactome | 8 / 37 | 118× | 1.12e-15 | 4.29e-13 ✓ sig. |
| Orc1 removal from chromatin | Reactome | 8 / 71 | 61.5× | 2.98e-13 | 7.01e-11 ✓ sig. |
| Cell cycle | KEGG | 9 / 158 | 31.1× | 4.04e-12 | 7.78e-10 ✓ sig. |
| CDT1 association with the CDC6:ORC:origin complex | Reactome | 6 / 59 | 55.5× | 7.60e-10 | 8.77e-8 ✓ sig. |
| CDC6 association with the ORC:origin complex | Reactome | 4 / 11 | 199× | 2.76e-9 | 2.77e-7 ✓ sig. |
| G1/S-Specific Transcription | Reactome | 4 / 24 | 91.0× | 8.76e-8 | 5.84e-6 ✓ sig. |
| Assembly of the ORC complex at the origin of replication | Reactome | 3 / 6 | 273× | 1.06e-7 | 6.90e-6 ✓ sig. |
| Switching of origins to a post-replicative state | Reactome | 3 / 6 | 273× | 1.06e-7 | 6.90e-6 ✓ sig. |
| DNA replication | KEGG | 3 / 36 | 45.5× | 3.66e-5 | 9.86e-4 ✓ sig. |
| WNT ligand biogenesis and trafficking | Reactome | 2 / 25 | 43.7× | 9.37e-4 | 1.29e-2 ✓ sig. |
| Signaling by FGFR2 amplification mutants | Reactome | 1 / 1 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| Signaling by FGFR2 fusions | Reactome | 1 / 1 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| Loss of MECP2 binding ability to 5mC-DNA | Reactome | 1 / 3 | 182× | 5.49e-3 | 4.65e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| DNA replication | GO:0006260 | 12 / 131 | 77.8× | 5.13e-21 | 9.64e-18 ✓ sig. |
| DNA replication initiation | GO:0006270 | 8 / 27 | 252× | 1.90e-18 | 2.44e-15 ✓ sig. |
| regulation of DNA-templated DNA replication initiation | GO:0030174 | 5 / 14 | 303× | 2.76e-12 | 1.15e-9 ✓ sig. |
| double-strand break repair via break-induced replication | GO:0000727 | 4 / 12 | 283× | 7.08e-10 | 1.65e-7 ✓ sig. |
| mitotic DNA replication checkpoint signaling | GO:0033314 | 3 / 11 | 232× | 2.32e-7 | 2.45e-5 ✓ sig. |
| DNA replication checkpoint signaling | GO:0000076 | 3 / 13 | 196× | 4.02e-7 | 3.89e-5 ✓ sig. |
| DNA replication preinitiation complex assembly | GO:0071163 | 2 / 2 | 849× | 1.32e-6 | 1.03e-4 ✓ sig. |
| negative regulation of DNA-templated DNA replication | GO:2000104 | 2 / 2 | 849× | 1.32e-6 | 1.03e-4 ✓ sig. |
| positive regulation of chromatin binding | GO:0035563 | 2 / 7 | 243× | 2.77e-5 | 1.15e-3 ✓ sig. |
| DNA strand elongation involved in DNA replication | GO:0006271 | 2 / 8 | 212× | 3.69e-5 | 1.43e-3 ✓ sig. |
| negative regulation of DNA replication | GO:0008156 | 2 / 16 | 106× | 1.57e-4 | 4.25e-3 ✓ sig. |
| replication fork processing | GO:0031297 | 2 / 41 | 41.4× | 1.06e-3 | 1.56e-2 ✓ sig. |
| response to methylglyoxal | GO:0051595 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| cellular response to tert-butyl hydroperoxide | GO:0072736 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| mitotic DNA replication preinitiation complex assembly | GO:1902977 | 1 / 1 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |