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 409
5
Diseases
2
Unique genes
0.405
Avg. similarity score
Bartsocas-papas syndrome
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Bartsocas-papas syndrome
Cocoon syndrome
Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency
bartsocas-papas syndrome 2
Curly hair ankyloblepharon nail dysplasia syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bartsocas-papas syndrome | 4 | 4 | 2 |
| Cocoon syndrome | 3 | 3 | 1 |
| Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency | 3 | 3 | 1 |
| bartsocas-papas syndrome 2 | 3 | 3 | 1 |
| Curly hair ankyloblepharon nail dysplasia syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CHUK | 4 / 5 | Bartsocas-papas syndrome, bartsocas-papas syndrome 2, Cocoon syndrome, Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency |
| RIPK4 | 2 / 5 | Bartsocas-papas syndrome, Curly hair ankyloblepharon nail dysplasia 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 | 2,002× | 5.00e-4 | 7.96e-3 ✓ sig. |
| IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) | Reactome | 1 / 3 | 2,002× | 5.00e-4 | 7.96e-3 ✓ sig. |
| IkBA variant leads to EDA-ID | Reactome | 1 / 7 | 858× | 1.17e-3 | 1.52e-2 ✓ sig. |
| AKT phosphorylates targets in the cytosol | Reactome | 1 / 11 | 546× | 1.83e-3 | 2.14e-2 ✓ sig. |
| NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 | Reactome | 1 / 12 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| MAP3K8 (TPL2)-dependent MAPK1/3 activation | Reactome | 1 / 14 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| IRAK1 recruits IKK complex | Reactome | 1 / 15 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation | Reactome | 1 / 15 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| RIP-mediated NFkB activation via ZBP1 | Reactome | 1 / 17 | 353× | 2.83e-3 | 2.95e-2 ✓ sig. |
| TICAM1, RIP1-mediated IKK complex recruitment | Reactome | 1 / 20 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| TRAF6 mediated NF-kB activation | Reactome | 1 / 24 | 250× | 3.99e-3 | 3.77e-2 ✓ sig. |
| Constitutive Signaling by AKT1 E17K in Cancer | Reactome | 1 / 25 | 240× | 4.16e-3 | 3.87e-2 ✓ sig. |
| IKK complex recruitment mediated by RIP1 | Reactome | 1 / 25 | 240× | 4.16e-3 | 3.87e-2 ✓ sig. |
| Antifolate resistance | KEGG | 1 / 30 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| ER-Phagosome pathway | Reactome | 1 / 30 | 200× | 4.99e-3 | 4.37e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of NF-kappaB transcription factor activity | GO:0051092 | 2 / 80 | 234× | 1.81e-5 | 8.30e-4 ✓ sig. |
| response to acetate | GO:0010034 | 1 / 1 | 9,344× | 1.07e-4 | 3.18e-3 ✓ sig. |
| response to cholecystokinin | GO:0061847 | 1 / 2 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| response to hydroperoxide | GO:0033194 | 1 / 9 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| striated muscle cell differentiation | GO:0051146 | 1 / 20 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| pattern recognition receptor signaling pathway | GO:0002221 | 1 / 21 | 445× | 2.25e-3 | 2.41e-2 ✓ sig. |
| response to amino acid | GO:0043200 | 1 / 22 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| positive regulation of interferon-alpha production | GO:0032727 | 1 / 26 | 359× | 2.78e-3 | 2.71e-2 ✓ sig. |
| skeletal muscle contraction | GO:0003009 | 1 / 32 | 292× | 3.42e-3 | 3.03e-2 ✓ sig. |
| non-canonical NF-kappaB signal transduction | GO:0038061 | 1 / 34 | 275× | 3.64e-3 | 3.14e-2 ✓ sig. |
| toll-like receptor 4 signaling pathway | GO:0034142 | 1 / 42 | 222× | 4.49e-3 | 3.47e-2 ✓ sig. |
| negative regulation of NF-kappaB transcription factor activity | GO:0032088 | 1 / 46 | 203× | 4.92e-3 | 3.63e-2 ✓ sig. |
| morphogenesis of an epithelium | GO:0002009 | 1 / 51 | 183× | 5.45e-3 | 3.84e-2 ✓ sig. |
| skin development | GO:0043588 | 1 / 55 | 170× | 5.88e-3 | 3.98e-2 ✓ sig. |
| tumor necrosis factor-mediated signaling pathway | GO:0033209 | 1 / 60 | 156× | 6.41e-3 | 4.15e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| bartsocas-papas syndrome 2 | Cocoon syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| bartsocas-papas syndrome 2 | Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Cocoon syndrome | Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Bartsocas-papas syndrome | Cocoon syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Bartsocas-papas syndrome | Combined immunodeficiency-hypogammaglobulinemia-skeletal anomalies syndrome due to ikbka deficiency | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Bartsocas-papas syndrome | bartsocas-papas syndrome 2 | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Bartsocas-papas syndrome | Curly hair ankyloblepharon nail dysplasia syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |