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 317
7
Diseases
10
Unique genes
0.223
Avg. similarity score
Abnormality of the cerebellum
Most-connected disease (4 links)
Disease
Searched: Neurodevelopmental disorder with cerebellar vermis hypoplasia
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Neurodevelopmental disorder with cerebellar vermis hypoplasia
Abnormality of the cerebellum
Generalized hypotonia
Hypoplasia of the corpus callosum
Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
Abnormality of the foot
Epileptic encephalopathy, early infantile, 66
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of the cerebellum | 4 | 4 | 2 |
| Generalized hypotonia | 4 | 4 | 8 |
| Hypoplasia of the corpus callosum | 4 | 4 | 2 |
| Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum | 3 | 3 | 1 |
| Abnormality of the foot | 1 | 1 | 1 |
| Epileptic encephalopathy, early infantile, 66 | 1 | 1 | 1 |
| Neurodevelopmental disorder with cerebellar vermis hypoplasia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LNPK | 4 / 7 | Abnormality of the cerebellum, Generalized hypotonia, Hypoplasia of the corpus callosum, Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum |
| ATG12 | 2 / 7 | Hypoplasia of the corpus callosum, Neurodevelopmental disorder with cerebellar vermis hypoplasia |
| PACS2 | 2 / 7 | Abnormality of the cerebellum, Epileptic encephalopathy, early infantile, 66 |
| SMARCD1 | 2 / 7 | Abnormality of the foot, Generalized hypotonia |
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 ⇵ |
|---|---|---|---|---|---|
| Toxicity of tetanus toxin (TeNT) | Reactome | 1 / 1 | 1,201× | 8.33e-4 | 9.85e-3 ✓ sig. |
| Nef mediated downregulation of CD28 cell surface expression | Reactome | 1 / 2 | 601× | 1.66e-3 | 1.66e-2 ✓ sig. |
| Synaptic vesicle cycle | KEGG | 2 / 79 | 30.4× | 1.86e-3 | 1.80e-2 ✓ sig. |
| Toxicity of botulinum toxin type B (BoNT/B) | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Toxicity of botulinum toxin type G (BoNT/G) | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Cargo recognition for clathrin-mediated endocytosis | Reactome | 2 / 106 | 22.7× | 3.32e-3 | 2.74e-2 ✓ sig. |
| Toxicity of botulinum toxin type D (BoNT/D) | Reactome | 1 / 5 | 240× | 4.16e-3 | 3.21e-2 ✓ sig. |
| Toxicity of botulinum toxin type F (BoNT/F) | Reactome | 1 / 5 | 240× | 4.16e-3 | 3.21e-2 ✓ sig. |
| Clathrin-mediated endocytosis | Reactome | 2 / 130 | 18.5× | 4.94e-3 | 3.64e-2 ✓ sig. |
| Nef Mediated CD8 Down-regulation | Reactome | 1 / 7 | 172× | 5.82e-3 | 4.03e-2 ✓ sig. |
| trans-Golgi Network Vesicle Budding | Reactome | 1 / 7 | 172× | 5.82e-3 | 4.03e-2 ✓ sig. |
| Nef Mediated CD4 Down-regulation | Reactome | 1 / 9 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Retrograde neurotrophin signalling | Reactome | 1 / 11 | 109× | 9.12e-3 | 5.37e-2 |
| Formation of annular gap junctions | Reactome | 1 / 11 | 109× | 9.12e-3 | 5.37e-2 |
| Receptor Mediated Mitophagy | Reactome | 1 / 11 | 109× | 9.12e-3 | 5.37e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| synaptic vesicle endocytosis | GO:0048488 | 2 / 41 | 91.2× | 2.09e-4 | 5.24e-3 ✓ sig. |
| establishment of natural killer cell polarity | GO:0001770 | 1 / 1 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| endoplasmic reticulum tubular network maintenance | GO:0071788 | 1 / 1 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| metanephric macula densa development | GO:0072227 | 1 / 1 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| metanephric DCT cell differentiation | GO:0072240 | 1 / 1 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| viral RNA genome packaging | GO:0019074 | 1 / 2 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| positive regulation of viral translation | GO:1904973 | 1 / 2 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| metanephric thick ascending limb development | GO:0072233 | 1 / 2 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| metanephric loop of Henle development | GO:0072236 | 1 / 2 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| regulation of delayed rectifier potassium channel activity | GO:1902259 | 1 / 2 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| autophagosome assembly | GO:0000045 | 2 / 98 | 38.1× | 1.19e-3 | 1.61e-2 ✓ sig. |
| regulation of histamine secretion by mast cell | GO:1903593 | 1 / 3 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| RNA-templated transcription | GO:0001172 | 1 / 3 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| forebrain ventricular zone progenitor cell division | GO:0021869 | 1 / 3 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of endoplasmic reticulum tubular network organization | GO:1903373 | 1 / 3 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |