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 179
8
Diseases
169
Unique genes
0.044
Avg. similarity score
Specific language disorder
Most-connected disease (5 links)
Disease
Searched: Language development disorders
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Language development disorders
Specific language disorder
Chromosome 2p16.3 deletion syndrome
Cortical dysplasia-focal epilepsy syndrome
Dyslexia
Internet addiction disorder
Male infertility acephalic spermatozoa
holocarboxylase synthetase deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Specific language disorder | 5 | 5 | 19 |
| Language development disorders | 4 | 4 | 26 |
| Chromosome 2p16.3 deletion syndrome | 2 | 2 | 1 |
| Cortical dysplasia-focal epilepsy syndrome | 2 | 2 | 1 |
| Dyslexia | 2 | 2 | 111 |
| Internet addiction disorder | 2 | 2 | 28 |
| Male infertility acephalic spermatozoa | 2 | 2 | 2 |
| holocarboxylase synthetase deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FOXP2 | 4 / 8 | Dyslexia, Internet addiction disorder, Language development disorders, Specific language disorder |
| NRXN1 | 4 / 8 | Chromosome 2p16.3 deletion syndrome, Dyslexia, Internet addiction disorder, Language development disorders |
| CNTNAP2 | 3 / 8 | Cortical dysplasia-focal epilepsy syndrome, Language development disorders, Specific language disorder |
| PMFBP1 | 3 / 8 | Dyslexia, Male infertility acephalic spermatozoa, Specific language disorder |
| CCDC136 | 2 / 8 | Dyslexia, Specific language disorder |
| COX6A1 | 2 / 8 | Dyslexia, Specific language disorder |
| DRD4 | 2 / 8 | Dyslexia, Internet addiction disorder |
| EPHA4 | 2 / 8 | Dyslexia, Specific language disorder |
| ERBB4 | 2 / 8 | Internet addiction disorder, Language development disorders |
| HLCS | 2 / 8 | holocarboxylase synthetase deficiency, Specific language disorder |
| INIP | 2 / 8 | Dyslexia, Specific language disorder |
| RBFOX2 | 2 / 8 | Dyslexia, Specific language disorder |
| STK24 | 2 / 8 | Dyslexia, Specific language disorder |
| ZFP64 | 2 / 8 | Dyslexia, Specific language disorder |
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 ⇵ |
|---|---|---|---|---|---|
| Dopaminergic synapse | KEGG | 11 / 132 | 5.9× | 2.46e-6 | 1.14e-4 ✓ sig. |
| Cocaine addiction | KEGG | 7 / 49 | 10.2× | 5.04e-6 | 2.04e-4 ✓ sig. |
| LDL remodeling | Reactome | 2 / 3 | 47.4× | 5.85e-4 | 9.33e-3 ✓ sig. |
| Cholesterol metabolism | KEGG | 5 / 51 | 7.0× | 7.24e-4 | 1.10e-2 ✓ sig. |
| Dopamine receptors | Reactome | 2 / 5 | 28.4× | 1.91e-3 | 2.29e-2 ✓ sig. |
| Chylomicron clearance | Reactome | 2 / 5 | 28.4× | 1.91e-3 | 2.29e-2 ✓ sig. |
| DARPP-32 events | Reactome | 3 / 19 | 11.2× | 2.25e-3 | 2.58e-2 ✓ sig. |
| Amphetamine addiction | KEGG | 5 / 69 | 5.1× | 2.83e-3 | 3.03e-2 ✓ sig. |
| Nuclear signaling by ERBB4 | Reactome | 3 / 24 | 8.9× | 4.46e-3 | 4.19e-2 ✓ sig. |
| Alcoholism | KEGG | 8 / 188 | 3.0× | 5.10e-3 | 4.59e-2 ✓ sig. |
| Chylomicron remodeling | Reactome | 2 / 9 | 15.8× | 6.64e-3 | 5.47e-2 |
| Chylomicron assembly | Reactome | 2 / 9 | 15.8× | 6.64e-3 | 5.47e-2 |
| HDL remodeling | Reactome | 2 / 10 | 14.2× | 8.22e-3 | 6.26e-2 |
| PI3K events in ERBB4 signaling | Reactome | 2 / 10 | 14.2× | 8.22e-3 | 6.26e-2 |
| Signaling by ERBB4 | Reactome | 2 / 11 | 12.9× | 9.96e-3 | 7.06e-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 ⇵ |
|---|---|---|---|---|---|
| vocal learning | GO:0042297 | 5 / 8 | 69.1× | 3.12e-9 | 6.13e-7 ✓ sig. |
| neuron migration | GO:0001764 | 11 / 132 | 9.2× | 3.21e-8 | 4.68e-6 ✓ sig. |
| adult behavior | GO:0030534 | 6 / 37 | 17.9× | 9.22e-7 | 7.91e-5 ✓ sig. |
| prepulse inhibition | GO:0060134 | 4 / 14 | 31.6× | 6.02e-6 | 3.61e-4 ✓ sig. |
| NMDA glutamate receptor clustering | GO:0097114 | 3 / 5 | 66.3× | 7.17e-6 | 4.14e-4 ✓ sig. |
| adenylate cyclase-inhibiting dopamine receptor signaling pathway | GO:0007195 | 3 / 5 | 66.3× | 7.17e-6 | 4.14e-4 ✓ sig. |
| response to amphetamine | GO:0001975 | 5 / 31 | 17.8× | 8.01e-6 | 4.54e-4 ✓ sig. |
| startle response | GO:0001964 | 4 / 18 | 24.6× | 1.79e-5 | 8.50e-4 ✓ sig. |
| vocalization behavior | GO:0071625 | 4 / 19 | 23.3× | 2.25e-5 | 1.02e-3 ✓ sig. |
| learning | GO:0007612 | 6 / 64 | 10.4× | 2.43e-5 | 1.07e-3 ✓ sig. |
| proteoglycan biosynthetic process | GO:0030166 | 4 / 21 | 21.1× | 3.43e-5 | 1.40e-3 ✓ sig. |
| negative regulation of protein secretion | GO:0050709 | 4 / 22 | 20.1× | 4.16e-5 | 1.62e-3 ✓ sig. |
| learning or memory | GO:0007611 | 6 / 72 | 9.2× | 4.77e-5 | 1.80e-3 ✓ sig. |
| postsynaptic density assembly | GO:0097107 | 3 / 9 | 36.9× | 5.86e-5 | 2.09e-3 ✓ sig. |
| nervous system development | GO:0007399 | 17 / 631 | 3.0× | 6.06e-5 | 2.15e-3 ✓ sig. |