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 212
8
Diseases
14
Unique genes
0.215
Avg. similarity score
Normal pressure hydrocephalus
Most-connected disease (5 links)
Disease
Searched: spermatogenic failure 56
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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spermatogenic failure 56
Normal pressure hydrocephalus
primary ciliary dyskinesia
Cerebelloparenchymal disorder
Lactic acidosis
Ptosis
spermatogenic failure 19
Young syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Normal pressure hydrocephalus | 5 | 5 | 2 |
| primary ciliary dyskinesia | 4 | 4 | 9 |
| Cerebelloparenchymal disorder | 3 | 3 | 1 |
| Lactic acidosis | 3 | 3 | 1 |
| Ptosis | 3 | 3 | 5 |
| spermatogenic failure 19 | 2 | 2 | 1 |
| Young syndrome | 1 | 1 | 1 |
| spermatogenic failure 56 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PMPCA | 4 / 8 | Cerebelloparenchymal disorder, Lactic acidosis, Normal pressure hydrocephalus, Ptosis |
| CFAP43 | 3 / 8 | Normal pressure hydrocephalus, primary ciliary dyskinesia, spermatogenic failure 19 |
| CFAP221 | 2 / 8 | primary ciliary dyskinesia, Young syndrome |
| DNAH10 | 2 / 8 | primary ciliary dyskinesia, spermatogenic failure 56 |
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 ⇵ |
|---|---|---|---|---|---|
| Motor proteins | KEGG | 3 / 194 | 13.3× | 1.32e-3 | 1.72e-2 ✓ sig. |
| Huntington disease | KEGG | 3 / 308 | 8.4× | 4.93e-3 | 4.42e-2 ✓ sig. |
| Amyotrophic lateral sclerosis | KEGG | 3 / 368 | 7.0× | 8.08e-3 | 6.13e-2 |
| Pathways of neurodegeneration - multiple diseases | KEGG | 3 / 480 | 5.4× | 1.66e-2 | 9.54e-2 |
| Processing of SMDT1 | Reactome | 1 / 16 | 53.6× | 1.85e-2 | 1.02e-1 |
| Transcriptional activation of mitochondrial biogenesis | Reactome | 1 / 51 | 16.8× | 5.79e-2 | 1.88e-1 |
| Lysine degradation | KEGG | 1 / 63 | 13.6× | 7.10e-2 | 2.10e-1 |
| RUNX1 regulates transcription of genes involved in differentiation of HSCs | Reactome | 1 / 69 | 12.4× | 7.75e-2 | 2.20e-1 |
| PKMTs methylate histone lysines | Reactome | 1 / 71 | 12.1× | 7.97e-2 | 2.23e-1 |
| RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function | Reactome | 1 / 97 | 8.8× | 1.07e-1 | 2.61e-1 |
| Spinocerebellar ataxia | KEGG | 1 / 144 | 6.0× | 1.55e-1 | 3.19e-1 |
| Cushing syndrome | KEGG | 1 / 155 | 5.5× | 1.66e-1 | 3.31e-1 |
| Transcriptional misregulation in cancer | KEGG | 1 / 198 | 4.3× | 2.08e-1 | 3.75e-1 |
| Metabolic pathways | KEGG | 1 / 1,563 | 0.5× | 8.58e-1 | 9.30e-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 ⇵ |
|---|---|---|---|---|---|
| cilium movement involved in cell motility | GO:0060294 | 4 / 27 | 198× | 3.42e-9 | 6.49e-7 ✓ sig. |
| cerebrospinal fluid circulation | GO:0090660 | 3 / 18 | 222× | 2.71e-7 | 2.84e-5 ✓ sig. |
| epithelial cilium movement involved in extracellular fluid movement | GO:0003351 | 3 / 26 | 154× | 8.62e-7 | 7.42e-5 ✓ sig. |
| sperm axoneme assembly | GO:0007288 | 3 / 31 | 129× | 1.49e-6 | 1.16e-4 ✓ sig. |
| cilium movement | GO:0003341 | 3 / 48 | 83.4× | 5.68e-6 | 3.38e-4 ✓ sig. |
| microtubule-based movement | GO:0007018 | 3 / 87 | 46.0× | 3.42e-5 | 1.37e-3 ✓ sig. |
| mucociliary clearance | GO:0120197 | 2 / 12 | 222× | 3.43e-5 | 1.37e-3 ✓ sig. |
| cilium-dependent cell motility | GO:0060285 | 2 / 12 | 222× | 3.43e-5 | 1.37e-3 ✓ sig. |
| inner dynein arm assembly | GO:0036159 | 2 / 18 | 148× | 7.92e-5 | 2.60e-3 ✓ sig. |
| establishment of localization in cell | GO:0051649 | 3 / 147 | 27.2× | 1.63e-4 | 4.44e-3 ✓ sig. |
| motile cilium assembly | GO:0044458 | 2 / 28 | 95.3× | 1.95e-4 | 5.07e-3 ✓ sig. |
| cell projection organization | GO:0030030 | 3 / 214 | 18.7× | 4.91e-4 | 9.64e-3 ✓ sig. |
| positive regulation of protein geranylgeranylation | GO:2000541 | 1 / 1 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| negative regulation of DNA methylation-dependent heterochromatin formation | GO:0090310 | 1 / 2 | 667× | 1.50e-3 | 1.95e-2 ✓ sig. |
| protein processing involved in protein targeting to mitochondrion | GO:0006627 | 1 / 5 | 267× | 3.74e-3 | 3.24e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cerebelloparenchymal disorder | Lactic acidosis | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Cerebelloparenchymal disorder | Normal pressure hydrocephalus | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| Lactic acidosis | Normal pressure hydrocephalus | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| Normal pressure hydrocephalus | spermatogenic failure 19 | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| Cerebelloparenchymal disorder | Ptosis | 0.167 | 1 | 3.25e-4 | 7.68e-4 ✓ sig. |
| Lactic acidosis | Ptosis | 0.167 | 1 | 3.25e-4 | 7.68e-4 ✓ sig. |
| primary ciliary dyskinesia | spermatogenic failure 56 | 0.100 | 1 | 5.84e-4 | 1.15e-3 ✓ sig. |
| primary ciliary dyskinesia | Young syndrome | 0.100 | 1 | 5.84e-4 | 1.15e-3 ✓ sig. |
| primary ciliary dyskinesia | spermatogenic failure 19 | 0.100 | 1 | 5.84e-4 | 1.15e-3 ✓ sig. |
| Normal pressure hydrocephalus | Ptosis | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |
| Normal pressure hydrocephalus | primary ciliary dyskinesia | 0.091 | 1 | 1.17e-3 | 1.89e-3 ✓ sig. |