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 523
5
Diseases
16
Unique genes
0.232
Avg. similarity score
Abnormality of the amniotic fluid
Most-connected disease (4 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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Abnormality of the amniotic fluid
Abnormality of the corpus callosum
Cerebral atrophy
Cns hypomyelination
Short long bone
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Abnormality of the amniotic fluid | 4 | 4 | 1 |
| Abnormality of the corpus callosum | 4 | 4 | 6 |
| Cerebral atrophy | 4 | 4 | 13 |
| Cns hypomyelination | 4 | 4 | 1 |
| Short long bone | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SLC35B2 | 5 / 5 | Abnormality of the amniotic fluid, Abnormality of the corpus callosum, Cerebral atrophy, Cns hypomyelination and 1 more |
| CACNA2D1 | 2 / 5 | Abnormality of the corpus callosum, Cerebral atrophy |
| DROSHA | 2 / 5 | Abnormality of the corpus callosum, Cerebral atrophy |
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 ⇵ |
|---|---|---|---|---|---|
| Defective PMM2 causes PMM2-CDG (CDG-1a) | Reactome | 1 / 1 | 751× | 1.33e-3 | 1.41e-2 ✓ sig. |
| RNA Polymerase II Transcription Elongation | Reactome | 2 / 59 | 25.4× | 2.72e-3 | 2.38e-2 ✓ sig. |
| Formation of RNA Pol II elongation complex | Reactome | 2 / 61 | 24.6× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Synthesis of GDP-mannose | Reactome | 1 / 3 | 250× | 3.99e-3 | 3.12e-2 ✓ sig. |
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 188× | 5.32e-3 | 3.80e-2 ✓ sig. |
| RNA Polymerase II Pre-transcription Events | Reactome | 2 / 84 | 17.9× | 5.44e-3 | 3.86e-2 ✓ sig. |
| Phosphonate and phosphinate metabolism | KEGG | 1 / 6 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Transport and synthesis of PAPS | Reactome | 1 / 6 | 125× | 7.97e-3 | 4.94e-2 ✓ sig. |
| Transport of nucleotide sugars | Reactome | 1 / 9 | 83.4× | 1.19e-2 | 6.32e-2 |
| Presynaptic depolarization and calcium channel opening | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 7.50e-2 |
| Synthesis of PE | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 7.50e-2 |
| Caspase-mediated cleavage of cytoskeletal proteins | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 7.50e-2 |
| TP53 Regulates Transcription of Caspase Activators and Caspases | Reactome | 1 / 12 | 62.6× | 1.59e-2 | 7.50e-2 |
| Purine salvage | Reactome | 1 / 13 | 57.7× | 1.72e-2 | 7.86e-2 |
| KSRP (KHSRP) binds and destabilizes mRNA | Reactome | 1 / 15 | 50.0× | 1.98e-2 | 8.52e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of growth rate | GO:0045967 | 1 / 1 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| guanosine metabolic process | GO:0008617 | 1 / 1 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| dGTP metabolic process | GO:0046070 | 1 / 1 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| purine deoxyribonucleoside metabolic process | GO:0046122 | 1 / 1 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| chromosomal DNA methylation maintenance following DNA replication | GO:0141119 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching | GO:1905931 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| regulation of cellular component size | GO:0032535 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| positive regulation of adherens junction organization | GO:1903393 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| GDP-D-mannose biosynthetic process from fructose-6-phosphate | GO:0061729 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| 3'-phosphoadenosine 5'-phosphosulfate transport | GO:0046963 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| 5'-adenylyl sulfate transmembrane transport | GO:1902558 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| 3'-phospho-5'-adenylyl sulfate transmembrane transport | GO:1902559 | 1 / 2 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| dAMP salvage | GO:0106383 | 1 / 3 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| GDP-mannose biosynthetic process from mannose | GO:0061728 | 1 / 3 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
| membrane depolarization during bundle of His cell action potential | GO:0086048 | 1 / 3 | 389× | 2.57e-3 | 2.40e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Abnormality of the corpus callosum | Cerebral atrophy | 0.176 | 3 | 9.23e-9 | 7.28e-8 ✓ sig. |
| Abnormality of the amniotic fluid | Short long bone | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Abnormality of the amniotic fluid | Cns hypomyelination | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Cns hypomyelination | Short long bone | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Abnormality of the amniotic fluid | Abnormality of the corpus callosum | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Abnormality of the corpus callosum | Cns hypomyelination | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Abnormality of the corpus callosum | Short long bone | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Abnormality of the amniotic fluid | Cerebral atrophy | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Cerebral atrophy | Cns hypomyelination | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |
| Cerebral atrophy | Short long bone | 0.071 | 1 | 8.39e-4 | 1.34e-3 ✓ sig. |