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 586
5
Diseases
5
Unique genes
0.367
Avg. similarity score
Cleft mandible
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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Cleft mandible
Microtia
Richieri costa pereira syndrome
Robin sequence
Robin sequence with cleft mandible and limb anomalies
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cleft mandible | 4 | 4 | 1 |
| Microtia | 4 | 4 | 5 |
| Richieri costa pereira syndrome | 4 | 4 | 1 |
| Robin sequence | 4 | 4 | 1 |
| Robin sequence with cleft mandible and limb anomalies | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| EIF4A3 | 5 / 5 | Cleft mandible, Microtia, Richieri costa pereira syndrome, Robin sequence and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation | Reactome | 1 / 13 | 185× | 5.40e-3 | 3.84e-2 ✓ sig. |
| Deadenylation of mRNA | Reactome | 1 / 24 | 100× | 9.95e-3 | 5.67e-2 |
| RNA Polymerase I Transcription Termination | Reactome | 1 / 32 | 75.1× | 1.33e-2 | 6.74e-2 |
| RNA polymerase | KEGG | 1 / 34 | 70.6× | 1.41e-2 | 6.99e-2 |
| RNA Polymerase I Transcription Initiation | Reactome | 1 / 45 | 53.4× | 1.86e-2 | 8.21e-2 |
| mRNA 3'-end processing | Reactome | 1 / 58 | 41.4× | 2.39e-2 | 9.49e-2 |
| RNA Polymerase II Transcription Termination | Reactome | 1 / 67 | 35.9× | 2.76e-2 | 1.03e-1 |
| ISG15 antiviral mechanism | Reactome | 1 / 72 | 33.4× | 2.96e-2 | 1.07e-1 |
| Transport of Mature mRNA derived from an Intron-Containing Transcript | Reactome | 1 / 75 | 32.0× | 3.08e-2 | 1.10e-1 |
| RNA Polymerase I Promoter Escape | Reactome | 1 / 91 | 26.4× | 3.73e-2 | 1.22e-1 |
| B-WICH complex positively regulates rRNA expression | Reactome | 1 / 91 | 26.4× | 3.73e-2 | 1.22e-1 |
| mRNA surveillance pathway | KEGG | 1 / 103 | 23.3× | 4.22e-2 | 1.31e-1 |
| Nucleocytoplasmic transport | KEGG | 1 / 108 | 22.2× | 4.42e-2 | 1.35e-1 |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | Reactome | 1 / 115 | 20.9× | 4.70e-2 | 1.40e-1 |
| Spliceosome | KEGG | 1 / 162 | 14.8× | 6.57e-2 | 1.69e-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 ⇵ |
|---|---|---|---|---|---|
| olfactory nerve development | GO:0021553 | 2 / 3 | 2,492× | 1.72e-7 | 1.99e-5 ✓ sig. |
| olfactory bulb development | GO:0021772 | 2 / 27 | 277× | 2.01e-5 | 9.25e-4 ✓ sig. |
| limb development | GO:0060173 | 2 / 56 | 133× | 8.77e-5 | 2.81e-3 ✓ sig. |
| inductive cell-cell signaling | GO:0031129 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| right ventricular compact myocardium morphogenesis | GO:0003226 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| cellular response to selenite ion | GO:0072715 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| negative regulation of selenocysteine incorporation | GO:1904570 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| rhombomere 3 morphogenesis | GO:0021658 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| olfactory bulb mitral cell layer development | GO:0061034 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| ureteric bud invasion | GO:0072092 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| rhombomere 2 development | GO:0021568 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| negative regulation of protein localization to nucleolus | GO:1904750 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| rRNA processing | GO:0006364 | 2 / 162 | 46.1× | 7.34e-4 | 1.23e-2 ✓ sig. |
| rhombomere 3 development | GO:0021569 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| brain segmentation | GO:0035284 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cleft mandible | Richieri costa pereira syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Cleft mandible | Robin sequence with cleft mandible and limb anomalies | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Cleft mandible | Robin sequence | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Richieri costa pereira syndrome | Robin sequence with cleft mandible and limb anomalies | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Richieri costa pereira syndrome | Robin sequence | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Robin sequence | Robin sequence with cleft mandible and limb anomalies | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Cleft mandible | Microtia | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Microtia | Richieri costa pereira syndrome | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Microtia | Robin sequence | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Microtia | Robin sequence with cleft mandible and limb anomalies | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |