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 278
7
Diseases
15
Unique genes
0.281
Avg. similarity score
Craniofacial microsomia
Most-connected disease (6 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Craniofacial microsomia
Deafness with congenital inner ear agenesis, microtia, and microdontia
Deafness with labyrinthine aplasia, microtia, and microdontia
Otodental dysplasia
Otodental syndrome
Corpus callosum agenesis with facial anomalies and cerebellar ataxia
Intestinal dysmotility syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Craniofacial microsomia | 6 | 6 | 15 |
| Deafness with congenital inner ear agenesis, microtia, and microdontia | 4 | 4 | 1 |
| Deafness with labyrinthine aplasia, microtia, and microdontia | 4 | 4 | 1 |
| Otodental dysplasia | 4 | 4 | 1 |
| Otodental syndrome | 4 | 4 | 1 |
| Corpus callosum agenesis with facial anomalies and cerebellar ataxia | 1 | 1 | 1 |
| Intestinal dysmotility syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FGF3 | 5 / 7 | Craniofacial microsomia, Deafness with congenital inner ear agenesis, microtia, and microdontia, Deafness with labyrinthine aplasia, microtia, and microdontia, Otodental dysplasia and 1 more |
| ANO1 | 2 / 7 | Craniofacial microsomia, Intestinal dysmotility syndrome |
| FRMD4A | 2 / 7 | Corpus callosum agenesis with facial anomalies and cerebellar ataxia, Craniofacial microsomia |
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 ⇵ |
|---|---|---|---|---|---|
| Late Phase of HIV Life Cycle | Reactome | 1 / 1 | 801× | 1.25e-3 | 1.60e-2 ✓ sig. |
| Cellular response to hypoxia | Reactome | 1 / 3 | 267× | 3.74e-3 | 3.59e-2 ✓ sig. |
| Activation, myristolyation of BID and translocation to mitochondria | Reactome | 1 / 4 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| PTK6 Expression | Reactome | 1 / 5 | 160× | 6.23e-3 | 5.06e-2 |
| FGFR1b ligand binding and activation | Reactome | 1 / 6 | 133× | 7.47e-3 | 5.69e-2 |
| FGFR2b ligand binding and activation | Reactome | 1 / 10 | 80.1× | 1.24e-2 | 7.78e-2 |
| Regulation of gene expression by Hypoxia-inducible Factor | Reactome | 1 / 11 | 72.8× | 1.37e-2 | 8.23e-2 |
| FGFRL1 modulation of FGFR1 signaling | Reactome | 1 / 13 | 61.6× | 1.61e-2 | 9.11e-2 |
| Phospholipase C-mediated cascade: FGFR1 | Reactome | 1 / 16 | 50.0× | 1.98e-2 | 1.02e-1 |
| Transcriptional regulation of pluripotent stem cells | Reactome | 1 / 17 | 47.1× | 2.10e-2 | 1.06e-1 |
| Activated point mutants of FGFR2 | Reactome | 1 / 17 | 47.1× | 2.10e-2 | 1.06e-1 |
| Phospholipase C-mediated cascade; FGFR2 | Reactome | 1 / 18 | 44.5× | 2.23e-2 | 1.09e-1 |
| Downstream signaling of activated FGFR1 | Reactome | 1 / 18 | 44.5× | 2.23e-2 | 1.09e-1 |
| PI-3K cascade:FGFR1 | Reactome | 1 / 21 | 38.1× | 2.59e-2 | 1.19e-1 |
| SHC-mediated cascade:FGFR1 | Reactome | 1 / 21 | 38.1× | 2.59e-2 | 1.19e-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 localization to membrane | GO:0072657 | 2 / 33 | 75.5× | 3.13e-4 | 6.93e-3 ✓ sig. |
| negative regulation of cardiac muscle tissue development | GO:0055026 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| N-terminal peptidyl-glycine N-myristoylation | GO:0018008 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| otic placode development | GO:1905040 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| cellular pigment accumulation | GO:0043482 | 1 / 2 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| glial cell projection elongation | GO:0106091 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| ketone metabolic process | GO:0042180 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| myoblast fate commitment | GO:0048625 | 1 / 3 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| positive regulation of establishment of protein localization to mitochondrion | GO:1903749 | 1 / 5 | 249× | 4.01e-3 | 3.28e-2 ✓ sig. |
| epidermal cell fate specification | GO:0009957 | 1 / 5 | 249× | 4.01e-3 | 3.28e-2 ✓ sig. |
| positive regulation of protein localization to lysosome | GO:0150032 | 1 / 6 | 208× | 4.81e-3 | 3.58e-2 ✓ sig. |
| parathyroid gland development | GO:0060017 | 1 / 7 | 178× | 5.61e-3 | 3.88e-2 ✓ sig. |
| iodide transport | GO:0015705 | 1 / 8 | 156× | 6.40e-3 | 4.15e-2 ✓ sig. |
| cellular response to peptide | GO:1901653 | 1 / 8 | 156× | 6.40e-3 | 4.15e-2 ✓ sig. |
| anatomical structure morphogenesis | GO:0009653 | 2 / 160 | 15.6× | 7.11e-3 | 4.37e-2 ✓ sig. |