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 581
5
Diseases
3
Unique genes
0.345
Avg. similarity score
Popliteal pterygium syndrome
Most-connected disease (4 links)
Disease
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Popliteal pterygium syndrome
Bartsocas-papas syndrome
Curly hair ankyloblepharon nail dysplasia syndrome
Popliteal pterygium syndrome, bartsocas-papas type 1
Condition
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Popliteal pterygium syndrome | 4 | 4 | 2 |
| Bartsocas-papas syndrome | 3 | 3 | 2 |
| Curly hair ankyloblepharon nail dysplasia syndrome | 3 | 3 | 1 |
| Popliteal pterygium syndrome, bartsocas-papas type 1 | 3 | 3 | 1 |
| Condition | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RIPK4 | 4 / 5 | Bartsocas-papas syndrome, Curly hair ankyloblepharon nail dysplasia syndrome, Popliteal pterygium syndrome, Popliteal pterygium syndrome, bartsocas-papas type 1 |
| IRF6 | 2 / 5 | Condition, Popliteal pterygium 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 ⇵ |
|---|---|---|---|---|---|
| IKBKB deficiency causes SCID | Reactome | 1 / 3 | 1,334× | 7.49e-4 | 9.09e-3 ✓ sig. |
| IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) | Reactome | 1 / 3 | 1,334× | 7.49e-4 | 9.09e-3 ✓ sig. |
| IkBA variant leads to EDA-ID | Reactome | 1 / 7 | 572× | 1.75e-3 | 1.73e-2 ✓ sig. |
| AKT phosphorylates targets in the cytosol | Reactome | 1 / 11 | 364× | 2.75e-3 | 2.39e-2 ✓ sig. |
| NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 | Reactome | 1 / 12 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| MAP3K8 (TPL2)-dependent MAPK1/3 activation | Reactome | 1 / 14 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| IRAK1 recruits IKK complex | Reactome | 1 / 15 | 267× | 3.74e-3 | 2.98e-2 ✓ sig. |
| IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation | Reactome | 1 / 15 | 267× | 3.74e-3 | 2.98e-2 ✓ sig. |
| RIP-mediated NFkB activation via ZBP1 | Reactome | 1 / 17 | 235× | 4.24e-3 | 3.26e-2 ✓ sig. |
| TICAM1, RIP1-mediated IKK complex recruitment | Reactome | 1 / 20 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| TRAF6 mediated NF-kB activation | Reactome | 1 / 24 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| Constitutive Signaling by AKT1 E17K in Cancer | Reactome | 1 / 25 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| IKK complex recruitment mediated by RIP1 | Reactome | 1 / 25 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| Antifolate resistance | KEGG | 1 / 30 | 133× | 7.48e-3 | 4.73e-2 ✓ sig. |
| ER-Phagosome pathway | Reactome | 1 / 30 | 133× | 7.48e-3 | 4.73e-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 ⇵ |
|---|---|---|---|---|---|
| skin development | GO:0043588 | 2 / 55 | 227× | 2.55e-5 | 1.11e-3 ✓ sig. |
| positive regulation of NF-kappaB transcription factor activity | GO:0051092 | 2 / 80 | 156× | 5.41e-5 | 1.96e-3 ✓ sig. |
| response to acetate | GO:0010034 | 1 / 1 | 6,229× | 1.61e-4 | 4.34e-3 ✓ sig. |
| response to cholecystokinin | GO:0061847 | 1 / 2 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| response to hydroperoxide | GO:0033194 | 1 / 9 | 692× | 1.44e-3 | 1.79e-2 ✓ sig. |
| mammary gland epithelial cell differentiation | GO:0060644 | 1 / 14 | 445× | 2.25e-3 | 2.24e-2 ✓ sig. |
| cranial skeletal system development | GO:1904888 | 1 / 18 | 346× | 2.89e-3 | 2.55e-2 ✓ sig. |
| striated muscle cell differentiation | GO:0051146 | 1 / 20 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| negative regulation of stem cell proliferation | GO:2000647 | 1 / 20 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| pattern recognition receptor signaling pathway | GO:0002221 | 1 / 21 | 297× | 3.37e-3 | 2.76e-2 ✓ sig. |
| response to amino acid | GO:0043200 | 1 / 22 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| negative regulation of keratinocyte proliferation | GO:0010839 | 1 / 24 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| positive regulation of interferon-alpha production | GO:0032727 | 1 / 26 | 240× | 4.17e-3 | 3.06e-2 ✓ sig. |
| keratinocyte proliferation | GO:0043616 | 1 / 29 | 215× | 4.65e-3 | 3.24e-2 ✓ sig. |
| skeletal muscle contraction | GO:0003009 | 1 / 32 | 195× | 5.13e-3 | 3.37e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Curly hair ankyloblepharon nail dysplasia syndrome | Popliteal pterygium syndrome, bartsocas-papas type 1 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Bartsocas-papas syndrome | Curly hair ankyloblepharon nail dysplasia syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Bartsocas-papas syndrome | Popliteal pterygium syndrome, bartsocas-papas type 1 | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Condition | Popliteal pterygium syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Curly hair ankyloblepharon nail dysplasia syndrome | Popliteal pterygium syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Popliteal pterygium syndrome | Popliteal pterygium syndrome, bartsocas-papas type 1 | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Bartsocas-papas syndrome | Popliteal pterygium syndrome | 0.250 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |