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 54
15
Diseases
55
Unique genes
0.091
Avg. similarity score
Situs ambiguus
Most-connected disease (9 links)
Disease
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Situs ambiguus
Heterotaxy syndrome
Situs inversus
Dextrocardia
Chylothorax
congenital heart disease with heterotaxy syndrome
Visceral heterotaxy
ciliary dyskinesia, primary, 40
Cardiac-urogenital syndrome
Ileocolitis
ciliary dyskinesia, primary, 38
primary ciliary dyskinesia 13
primary ciliary dyskinesia 19
primary ciliary dyskinesia 26
primary ciliary dyskinesia 35
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Situs ambiguus | 9 | 9 | 21 |
| Heterotaxy syndrome | 7 | 7 | 22 |
| Situs inversus | 7 | 7 | 20 |
| Dextrocardia | 4 | 4 | 7 |
| Chylothorax | 3 | 3 | 1 |
| congenital heart disease with heterotaxy syndrome | 3 | 3 | 2 |
| Visceral heterotaxy | 2 | 2 | 4 |
| ciliary dyskinesia, primary, 40 | 2 | 2 | 1 |
| Cardiac-urogenital syndrome | 1 | 1 | 1 |
| Ileocolitis | 1 | 1 | 8 |
| ciliary dyskinesia, primary, 38 | 1 | 1 | 1 |
| primary ciliary dyskinesia 13 | 1 | 1 | 1 |
| primary ciliary dyskinesia 19 | 1 | 1 | 1 |
| primary ciliary dyskinesia 26 | 1 | 1 | 1 |
| primary ciliary dyskinesia 35 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CFAP53 | 4 / 15 | Dextrocardia, Heterotaxy syndrome, Situs ambiguus, Situs inversus |
| NODAL | 4 / 15 | congenital heart disease with heterotaxy syndrome, Heterotaxy syndrome, Situs ambiguus, Situs inversus |
| PKD1L1 | 4 / 15 | Chylothorax, Heterotaxy syndrome, Situs ambiguus, Situs inversus |
| ZIC3 | 4 / 15 | congenital heart disease with heterotaxy syndrome, Dextrocardia, Heterotaxy syndrome, Situs inversus |
| CFAP52 | 3 / 15 | Heterotaxy syndrome, Situs inversus, Visceral heterotaxy |
| CIROP | 3 / 15 | Heterotaxy syndrome, Situs ambiguus, Situs inversus |
| DNAH9 | 3 / 15 | ciliary dyskinesia, primary, 40, Situs ambiguus, Situs inversus |
| MMP21 | 3 / 15 | Heterotaxy syndrome, Situs ambiguus, Situs inversus |
| ACVR2B | 2 / 15 | Heterotaxy syndrome, Situs inversus |
| CERS1 | 2 / 15 | Heterotaxy syndrome, Situs ambiguus |
| CFAP298 | 2 / 15 | primary ciliary dyskinesia 26, Situs ambiguus |
| CFAP300 | 2 / 15 | ciliary dyskinesia, primary, 38, Situs ambiguus |
| CFAP45 | 2 / 15 | Heterotaxy syndrome, Ileocolitis |
| CIROZ | 2 / 15 | Heterotaxy syndrome, Visceral heterotaxy |
| DAND5 | 2 / 15 | Heterotaxy syndrome, Situs ambiguus |
| DAW1 | 2 / 15 | Heterotaxy syndrome, Visceral heterotaxy |
| DNAAF1 | 2 / 15 | primary ciliary dyskinesia 13, Situs ambiguus |
| DNAAF11 | 2 / 15 | primary ciliary dyskinesia 19, Situs ambiguus |
| DNAH5 | 2 / 15 | Situs ambiguus, Situs inversus |
| GDF1 | 2 / 15 | Heterotaxy syndrome, Situs ambiguus |
| LEFTY2 | 2 / 15 | Heterotaxy syndrome, Visceral heterotaxy |
| MNS1 | 2 / 15 | Heterotaxy syndrome, Situs inversus |
| MYRF | 2 / 15 | Cardiac-urogenital syndrome, Dextrocardia |
| ODAD4 | 2 / 15 | primary ciliary dyskinesia 35, Situs ambiguus |
| TEX9 | 2 / 15 | Heterotaxy syndrome, Situs inversus |
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 ⇵ |
|---|---|---|---|---|---|
| TGF-beta signaling pathway | KEGG | 4 / 108 | 8.1× | 1.48e-3 | 1.83e-2 ✓ sig. |
| Motor proteins | KEGG | 5 / 194 | 5.6× | 1.89e-3 | 2.19e-2 ✓ sig. |
| Transcriptional regulation of pluripotent stem cells | Reactome | 2 / 17 | 25.7× | 2.68e-3 | 2.84e-2 ✓ sig. |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 4 / 144 | 6.1× | 4.21e-3 | 3.91e-2 ✓ sig. |
| Signaling by BMP | Reactome | 2 / 28 | 15.6× | 7.21e-3 | 5.58e-2 |
| Huntington disease | KEGG | 5 / 308 | 3.5× | 1.31e-2 | 8.03e-2 |
| RHO GTPases Activate ROCKs | Reactome | 1 / 5 | 43.7× | 2.27e-2 | 1.10e-1 |
| Amyotrophic lateral sclerosis | KEGG | 5 / 368 | 3.0× | 2.61e-2 | 1.19e-1 |
| Sema4D induced cell migration and growth-cone collapse | Reactome | 1 / 11 | 19.9× | 4.93e-2 | 1.70e-1 |
| Signaling by Activin | Reactome | 1 / 11 | 19.9× | 4.93e-2 | 1.70e-1 |
| POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation | Reactome | 1 / 13 | 16.8× | 5.80e-2 | 1.85e-1 |
| Pathways of neurodegeneration - multiple diseases | KEGG | 5 / 480 | 2.3× | 6.79e-2 | 2.01e-1 |
| Chromatin modifying enzymes | Reactome | 1 / 20 | 10.9× | 8.78e-2 | 2.31e-1 |
| Sphingolipid signaling pathway | KEGG | 2 / 122 | 3.6× | 1.07e-1 | 2.58e-1 |
| Platelet degranulation | Reactome | 2 / 123 | 3.6× | 1.09e-1 | 2.60e-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 ⇵ |
|---|---|---|---|---|---|
| determination of left/right symmetry | GO:0007368 | 15 / 83 | 61.4× | 1.40e-23 | 3.83e-20 ✓ sig. |
| epithelial cilium movement involved in determination of left/right asymmetry | GO:0060287 | 8 / 13 | 209× | 4.21e-18 | 5.13e-15 ✓ sig. |
| cilium movement | GO:0003341 | 10 / 48 | 70.8× | 1.23e-16 | 1.14e-13 ✓ sig. |
| epithelial cilium movement involved in extracellular fluid movement | GO:0003351 | 7 / 26 | 91.5× | 8.11e-13 | 3.80e-10 ✓ sig. |
| cerebrospinal fluid circulation | GO:0090660 | 6 / 18 | 113× | 8.86e-12 | 3.29e-9 ✓ sig. |
| flagellated sperm motility | GO:0030317 | 10 / 142 | 23.9× | 1.02e-11 | 3.75e-9 ✓ sig. |
| cilium movement involved in cell motility | GO:0060294 | 6 / 27 | 75.5× | 1.39e-10 | 3.86e-8 ✓ sig. |
| determination of pancreatic left/right asymmetry | GO:0035469 | 4 / 5 | 272× | 3.35e-10 | 8.44e-8 ✓ sig. |
| heart development | GO:0007507 | 11 / 273 | 13.7× | 3.58e-10 | 8.96e-8 ✓ sig. |
| axonemal dynein complex assembly | GO:0070286 | 5 / 16 | 106× | 7.81e-10 | 1.80e-7 ✓ sig. |
| determination of liver left/right asymmetry | GO:0071910 | 4 / 6 | 227× | 1.00e-9 | 2.25e-7 ✓ sig. |
| determination of digestive tract left/right asymmetry | GO:0071907 | 4 / 6 | 227× | 1.00e-9 | 2.25e-7 ✓ sig. |
| inner dynein arm assembly | GO:0036159 | 5 / 18 | 94.4× | 1.53e-9 | 3.27e-7 ✓ sig. |
| outer dynein arm assembly | GO:0036158 | 5 / 22 | 77.2× | 4.65e-9 | 8.74e-7 ✓ sig. |
| regulation of cilium beat frequency | GO:0003356 | 4 / 8 | 170× | 4.66e-9 | 8.76e-7 ✓ sig. |