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 226
7
Diseases
24
Unique genes
0.328
Avg. similarity score
Uranostaphyloschisis
Most-connected disease (6 links)
Disease
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Uranostaphyloschisis
Abruzzo-erickson syndrome
Cleft palate with ankyloglossia
Cleft palate x-linked
X-linked cleft palate and ankloglossia
cleft palate with or without ankyloglossia, x-linked
fanconi anemia complementation group d2
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Uranostaphyloschisis | 6 | 6 | 24 |
| Abruzzo-erickson syndrome | 5 | 5 | 1 |
| Cleft palate with ankyloglossia | 5 | 5 | 1 |
| Cleft palate x-linked | 5 | 5 | 1 |
| X-linked cleft palate and ankloglossia | 5 | 5 | 1 |
| cleft palate with or without ankyloglossia, x-linked | 5 | 5 | 1 |
| fanconi anemia complementation group d2 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TBX22 | 6 / 7 | Abruzzo-erickson syndrome, Cleft palate with ankyloglossia, cleft palate with or without ankyloglossia, x-linked, Cleft palate x-linked and 2 more |
| FANCD2 | 2 / 7 | fanconi anemia complementation group d2, Uranostaphyloschisis |
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 ⇵ |
|---|---|---|---|---|---|
| ARL13B-mediated ciliary trafficking of INPP5E | Reactome | 1 / 3 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| SUMOylation of chromatin organization proteins | Reactome | 2 / 70 | 14.3× | 8.51e-3 | 6.22e-2 |
| Inositol phosphate metabolism | KEGG | 2 / 73 | 13.7× | 9.22e-3 | 6.54e-2 |
| MyD88 dependent cascade initiated on endosome | Reactome | 1 / 8 | 62.6× | 1.59e-2 | 9.02e-2 |
| Phosphatidylinositol signaling system | KEGG | 2 / 98 | 10.2× | 1.62e-2 | 9.12e-2 |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 55.6× | 1.78e-2 | 9.67e-2 |
| OAS antiviral response | Reactome | 1 / 9 | 55.6× | 1.78e-2 | 9.67e-2 |
| MyD88 cascade initiated on plasma membrane | Reactome | 1 / 9 | 55.6× | 1.78e-2 | 9.67e-2 |
| Cohesin Loading onto Chromatin | Reactome | 1 / 10 | 50.0× | 1.98e-2 | 1.02e-1 |
| TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation | Reactome | 1 / 10 | 50.0× | 1.98e-2 | 1.02e-1 |
| Cell-extracellular matrix interactions | Reactome | 1 / 12 | 41.7× | 2.37e-2 | 1.13e-1 |
| GP1b-IX-V activation signalling | Reactome | 1 / 12 | 41.7× | 2.37e-2 | 1.13e-1 |
| Synthesis of IP2, IP, and Ins in the cytosol | Reactome | 1 / 12 | 41.7× | 2.37e-2 | 1.13e-1 |
| p75NTR recruits signalling complexes | Reactome | 1 / 13 | 38.5× | 2.57e-2 | 1.18e-1 |
| NF-kB is activated and signals survival | Reactome | 1 / 13 | 38.5× | 2.57e-2 | 1.18e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of neuron migration | GO:2001224 | 2 / 16 | 97.3× | 1.88e-4 | 4.84e-3 ✓ sig. |
| cartilage development | GO:0051216 | 3 / 89 | 26.2× | 1.97e-4 | 4.99e-3 ✓ sig. |
| phosphate-containing compound metabolic process | GO:0006796 | 2 / 25 | 62.3× | 4.66e-4 | 9.12e-3 ✓ sig. |
| chromatin remodeling | GO:0006338 | 4 / 320 | 9.7× | 6.84e-4 | 1.18e-2 ✓ sig. |
| embryonic pattern specification | GO:0009880 | 2 / 32 | 48.7× | 7.66e-4 | 1.27e-2 ✓ sig. |
| face morphogenesis | GO:0060325 | 2 / 33 | 47.2× | 8.15e-4 | 1.32e-2 ✓ sig. |
| homologous chromosome pairing at meiosis | GO:0007129 | 2 / 33 | 47.2× | 8.15e-4 | 1.32e-2 ✓ sig. |
| regulation of membrane repolarization during atrial cardiac muscle cell action potential | GO:1905000 | 1 / 1 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| regulation of membrane repolarization during cardiac muscle cell action potential | GO:1905031 | 1 / 1 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| mitochondrion migration along actin filament | GO:0034642 | 1 / 1 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| external genitalia morphogenesis | GO:0035261 | 1 / 1 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 7 / 1,454 | 3.7× | 1.81e-3 | 2.15e-2 ✓ sig. |
| embryonic skeletal system morphogenesis | GO:0048704 | 2 / 53 | 29.4× | 2.09e-3 | 2.32e-2 ✓ sig. |
| regulation of calcium ion-dependent exocytosis of neurotransmitter | GO:1903233 | 1 / 2 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| regulation of developmental growth | GO:0048638 | 1 / 2 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |