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 355
6
Diseases
13
Unique genes
0.081
Avg. similarity score
Hyperphosphatasia with intellectual disability syndrome
Most-connected disease (5 links)
Disease
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Hyperphosphatasia with intellectual disability syndrome
Intellectual developmental disorder dysmorphic facial
developmental and epileptic encephalopathy, 80
hyperphosphatasia with intellectual disability syndrome 1
hyperphosphatasia with intellectual disability syndrome 4
hyperphosphatasia with intellectual disability syndrome 6
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Hyperphosphatasia with intellectual disability syndrome | 5 | 5 | 11 |
| Intellectual developmental disorder dysmorphic facial | 1 | 1 | 3 |
| developmental and epileptic encephalopathy, 80 | 1 | 1 | 1 |
| hyperphosphatasia with intellectual disability syndrome 1 | 1 | 1 | 1 |
| hyperphosphatasia with intellectual disability syndrome 4 | 1 | 1 | 1 |
| hyperphosphatasia with intellectual disability syndrome 6 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PGAP3 | 2 / 6 | Hyperphosphatasia with intellectual disability syndrome, hyperphosphatasia with intellectual disability syndrome 4 |
| PIGB | 2 / 6 | developmental and epileptic encephalopathy, 80, Hyperphosphatasia with intellectual disability syndrome |
| PIGV | 2 / 6 | Hyperphosphatasia with intellectual disability syndrome, hyperphosphatasia with intellectual disability syndrome 1 |
| PIGY | 2 / 6 | Hyperphosphatasia with intellectual disability syndrome, hyperphosphatasia with intellectual disability syndrome 6 |
| SETD5 | 2 / 6 | Hyperphosphatasia with intellectual disability syndrome, Intellectual developmental disorder dysmorphic facial |
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 ⇵ |
|---|---|---|---|---|---|
| Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | KEGG | 9 / 30 | 277× | 7.12e-22 | 7.94e-19 ✓ sig. |
| Synthesis of glycosylphosphatidylinositol (GPI) | Reactome | 6 / 17 | 326× | 5.07e-15 | 1.71e-12 ✓ sig. |
| Metabolic pathways | KEGG | 9 / 1,563 | 5.3× | 4.58e-6 | 1.77e-4 ✓ sig. |
| SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription | Reactome | 1 / 32 | 28.9× | 3.41e-2 | 1.39e-1 |
| RNA Polymerase II Transcription Elongation | Reactome | 1 / 59 | 15.7× | 6.20e-2 | 1.92e-1 |
| Formation of RNA Pol II elongation complex | Reactome | 1 / 61 | 15.1× | 6.41e-2 | 1.95e-1 |
| TP53 Regulates Transcription of DNA Repair Genes | Reactome | 1 / 65 | 14.2× | 6.82e-2 | 2.01e-1 |
| RNA polymerase II transcribes snRNA genes | Reactome | 1 / 74 | 12.5× | 7.72e-2 | 2.15e-1 |
| RNA Polymerase II Pre-transcription Events | Reactome | 1 / 84 | 11.0× | 8.72e-2 | 2.30e-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 ⇵ |
|---|---|---|---|---|---|
| GPI anchor biosynthetic process | GO:0006506 | 9 / 31 | 417× | 1.88e-23 | 5.05e-20 ✓ sig. |
| GPI anchor metabolic process | GO:0006505 | 2 / 2 | 1,437× | 4.47e-7 | 4.25e-5 ✓ sig. |
| negative regulation of transcription by RNA polymerase III | GO:0016480 | 1 / 4 | 359× | 2.78e-3 | 2.71e-2 ✓ sig. |
| regulation of DNA-templated transcription elongation | GO:0032784 | 1 / 7 | 205× | 4.86e-3 | 3.60e-2 ✓ sig. |
| radial glial cell differentiation | GO:0060019 | 1 / 8 | 180× | 5.55e-3 | 3.87e-2 ✓ sig. |
| regulation of chromatin organization | GO:1902275 | 1 / 11 | 131× | 7.63e-3 | 4.52e-2 ✓ sig. |
| positive regulation of DNA-templated transcription, elongation | GO:0032786 | 1 / 13 | 111× | 9.01e-3 | 4.86e-2 ✓ sig. |
| host-mediated suppression of viral genome replication | GO:0044828 | 1 / 13 | 111× | 9.01e-3 | 4.86e-2 ✓ sig. |
| regulation of cyclin-dependent protein serine/threonine kinase activity | GO:0000079 | 1 / 22 | 65.3× | 1.52e-2 | 6.27e-2 |
| regulation of synapse assembly | GO:0051963 | 1 / 29 | 49.6× | 2.00e-2 | 7.18e-2 |
| establishment of cell polarity | GO:0030010 | 1 / 46 | 31.2× | 3.15e-2 | 9.04e-2 |
| establishment of protein localization | GO:0045184 | 1 / 51 | 28.2× | 3.49e-2 | 9.55e-2 |
| positive regulation of transcription elongation by RNA polymerase II | GO:0032968 | 1 / 57 | 25.2× | 3.89e-2 | 1.01e-1 |
| cognition | GO:0050890 | 1 / 64 | 22.5× | 4.36e-2 | 1.07e-1 |
| cerebral cortex development | GO:0021987 | 1 / 88 | 16.3× | 5.95e-2 | 1.27e-1 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| developmental and epileptic encephalopathy, 80 | Hyperphosphatasia with intellectual disability syndrome | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Hyperphosphatasia with intellectual disability syndrome | hyperphosphatasia with intellectual disability syndrome 4 | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Hyperphosphatasia with intellectual disability syndrome | hyperphosphatasia with intellectual disability syndrome 1 | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Hyperphosphatasia with intellectual disability syndrome | hyperphosphatasia with intellectual disability syndrome 6 | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Hyperphosphatasia with intellectual disability syndrome | Intellectual developmental disorder dysmorphic facial | 0.071 | 1 | 2.14e-3 | 3.03e-3 ✓ sig. |