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 498
6
Diseases
5
Unique genes
0.325
Avg. similarity score
Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Most-connected disease (4 links)
Disease
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Deafness, autosomal recessive 4, with enlarged vestibular aqueduct
Deafness, autosomal recessive, 4
Mondini defect
Sensorineural deafness
Goitre
Winkelman bethge pfeiffer syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Deafness, autosomal recessive 4, with enlarged vestibular aqueduct | 4 | 4 | 1 |
| Deafness, autosomal recessive, 4 | 4 | 4 | 1 |
| Mondini defect | 4 | 4 | 1 |
| Sensorineural deafness | 4 | 4 | 3 |
| Goitre | 3 | 3 | 3 |
| Winkelman bethge pfeiffer syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SLC26A4 | 5 / 6 | Deafness, autosomal recessive 4, with enlarged vestibular aqueduct, Deafness, autosomal recessive, 4, Goitre, Mondini defect and 1 more |
| LHX3 | 2 / 6 | Sensorineural deafness, Winkelman bethge pfeiffer syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Thyroid hormone synthesis | KEGG | 3 / 75 | 96.1× | 2.32e-6 | 8.56e-5 ✓ sig. |
| Thyroxine biosynthesis | Reactome | 2 / 7 | 686× | 2.91e-6 | 1.04e-4 ✓ sig. |
| Defective SLC26A4 causes Pendred syndrome (PDS) | Reactome | 1 / 1 | 2,402× | 4.16e-4 | 5.79e-3 ✓ sig. |
| Defective SLC5A5 causes thyroid dyshormonogenesis 1 (TDH1) | Reactome | 1 / 1 | 2,402× | 4.16e-4 | 5.79e-3 ✓ sig. |
| Multifunctional anion exchangers | Reactome | 1 / 9 | 267× | 3.74e-3 | 2.98e-2 ✓ sig. |
| Organic anion transporters | Reactome | 1 / 10 | 240× | 4.16e-3 | 3.21e-2 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| iodide transport | GO:0015705 | 2 / 8 | 934× | 1.60e-6 | 1.27e-4 ✓ sig. |
| thyroid hormone generation | GO:0006590 | 2 / 16 | 467× | 6.86e-6 | 4.06e-4 ✓ sig. |
| prolactin secreting cell differentiation | GO:0060127 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| medial motor column neuron differentiation | GO:0021526 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| iodide transmembrane transport | GO:1904200 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| cellular response to Thyroid stimulating hormone | GO:1904401 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| cuticle development | GO:0042335 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| ventral spinal cord interneuron specification | GO:0021521 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| somatotropin secreting cell differentiation | GO:0060126 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| thyroid-stimulating hormone-secreting cell differentiation | GO:0060129 | 1 / 6 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| cellular response to gonadotropin stimulus | GO:0071371 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| spinal cord motor neuron cell fate specification | GO:0021520 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
| hydrogen peroxide biosynthetic process | GO:0050665 | 1 / 11 | 340× | 2.94e-3 | 2.58e-2 ✓ sig. |
| oxalate transport | GO:0019532 | 1 / 11 | 340× | 2.94e-3 | 2.58e-2 ✓ sig. |
| hormone biosynthetic process | GO:0042446 | 1 / 12 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Deafness, autosomal recessive 4, with enlarged vestibular aqueduct | Mondini defect | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Deafness, autosomal recessive 4, with enlarged vestibular aqueduct | Deafness, autosomal recessive, 4 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Deafness, autosomal recessive, 4 | Mondini defect | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Deafness, autosomal recessive 4, with enlarged vestibular aqueduct | Goitre | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Deafness, autosomal recessive 4, with enlarged vestibular aqueduct | Sensorineural deafness | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Deafness, autosomal recessive, 4 | Goitre | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Deafness, autosomal recessive, 4 | Sensorineural deafness | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Goitre | Mondini defect | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Mondini defect | Sensorineural deafness | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Sensorineural deafness | Winkelman bethge pfeiffer syndrome | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |