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 19
21
Diseases
71
Unique genes
0.118
Avg. similarity score
Short-rib thoracic dysplasia
Most-connected disease (16 links)
Disease
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Short-rib thoracic dysplasia
Short rib dysplasia-polydactyly syndrome
Jeune thoracic dystrophy
Jeune syndrome
Saldino-noonan syndrome
Majewski syndrome
Craniodiaphyseal dysplasia
short-rib thoracic dysplasia 11 with or without polydactyly
short-rib thoracic dysplasia 16 with or without polydactyly
short-rib thoracic dysplasia 17 with or without polydactyly
amyotrophic lateral sclerosis, susceptibility to, 24
nephronophthisis 12
short-rib thoracic dysplasia 8 with or without polydactyly
INTU-related skeletal ciliopathy
short-rib thoracic dysplasia 19 with or without polydactyly
Developmental delay with or without epilepsy
cranioectodermal dysplasia 1
BBS10-related ciliopathy
NIK deficiency
Thoracic malformation
dilated cardiomyopathy 1V
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Short-rib thoracic dysplasia | 16 | 16 | 23 |
| Short rib dysplasia-polydactyly syndrome | 15 | 15 | 24 |
| Jeune thoracic dystrophy | 14 | 14 | 33 |
| Jeune syndrome | 10 | 10 | 42 |
| Saldino-noonan syndrome | 10 | 10 | 10 |
| Majewski syndrome | 7 | 7 | 12 |
| Craniodiaphyseal dysplasia | 5 | 5 | 10 |
| short-rib thoracic dysplasia 11 with or without polydactyly | 5 | 5 | 1 |
| short-rib thoracic dysplasia 16 with or without polydactyly | 5 | 5 | 1 |
| short-rib thoracic dysplasia 17 with or without polydactyly | 5 | 5 | 1 |
| amyotrophic lateral sclerosis, susceptibility to, 24 | 4 | 4 | 1 |
| nephronophthisis 12 | 4 | 4 | 1 |
| short-rib thoracic dysplasia 8 with or without polydactyly | 4 | 4 | 1 |
| INTU-related skeletal ciliopathy | 3 | 3 | 1 |
| short-rib thoracic dysplasia 19 with or without polydactyly | 3 | 3 | 1 |
| Developmental delay with or without epilepsy | 2 | 2 | 1 |
| cranioectodermal dysplasia 1 | 2 | 2 | 1 |
| BBS10-related ciliopathy | 1 | 1 | 1 |
| NIK deficiency | 1 | 1 | 1 |
| Thoracic malformation | 1 | 1 | 1 |
| dilated cardiomyopathy 1V | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NEK1 | 7 / 21 | amyotrophic lateral sclerosis, susceptibility to, 24, Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome and 3 more |
| DYNC2H1 | 6 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome, Saldino-noonan syndrome and 2 more |
| DYNC2I1 | 6 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Saldino-noonan syndrome, Short rib dysplasia-polydactyly syndrome and 2 more |
| DYNC2I2 | 6 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Saldino-noonan syndrome, Short rib dysplasia-polydactyly syndrome and 2 more |
| DYNLT2B | 6 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Saldino-noonan syndrome, Short rib dysplasia-polydactyly syndrome and 2 more |
| IFT52 | 6 / 21 | Craniodiaphyseal dysplasia, Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome and 2 more |
| TTC21B | 6 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome, nephronophthisis 12 and 2 more |
| WDR35 | 6 / 21 | Craniodiaphyseal dysplasia, Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome and 2 more |
| DYNC2LI1 | 5 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome, Short rib dysplasia-polydactyly syndrome and 1 more |
| IFT140 | 5 / 21 | Craniodiaphyseal dysplasia, Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome and 1 more |
| IFT172 | 5 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome, Short rib dysplasia-polydactyly syndrome and 1 more |
| IFT80 | 5 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Majewski syndrome, Short rib dysplasia-polydactyly syndrome and 1 more |
| INTU | 5 / 21 | INTU-related skeletal ciliopathy, Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome and 1 more |
| WDR19 | 5 / 21 | Craniodiaphyseal dysplasia, Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome and 1 more |
| CEP120 | 4 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome, Short-rib thoracic dysplasia |
| IFT43 | 4 / 21 | Craniodiaphyseal dysplasia, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome, Short-rib thoracic dysplasia |
| IFT81 | 4 / 21 | Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome, Short-rib thoracic dysplasia, short-rib thoracic dysplasia 19 with or without polydactyly |
| KIAA0586 | 4 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome, Short-rib thoracic dysplasia |
| KIAA0753 | 4 / 21 | Jeune syndrome, Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome, Short-rib thoracic dysplasia |
| EVC2 | 3 / 21 | Jeune thoracic dystrophy, Majewski syndrome, Short rib dysplasia-polydactyly syndrome |
| IFT122 | 3 / 21 | Craniodiaphyseal dysplasia, cranioectodermal dysplasia 1, Short rib dysplasia-polydactyly syndrome |
| SPTAN1 | 3 / 21 | Developmental delay with or without epilepsy, Jeune thoracic dystrophy, Short-rib thoracic dysplasia |
| TRAF3IP1 | 3 / 21 | Jeune thoracic dystrophy, Majewski syndrome, Short rib dysplasia-polydactyly syndrome |
| BBS10 | 2 / 21 | BBS10-related ciliopathy, Saldino-noonan syndrome |
| CILK1 | 2 / 21 | Craniodiaphyseal dysplasia, Short rib dysplasia-polydactyly syndrome |
| FGF4 | 2 / 21 | Short-rib thoracic dysplasia, Thoracic malformation |
| FLVCR1 | 2 / 21 | Jeune thoracic dystrophy, Short rib dysplasia-polydactyly syndrome |
| FUZ | 2 / 21 | Jeune thoracic dystrophy, Majewski syndrome |
| GRK2 | 2 / 21 | Jeune syndrome, Jeune thoracic dystrophy |
| IFT74 | 2 / 21 | Jeune thoracic dystrophy, Majewski syndrome |
| MAP3K14 | 2 / 21 | Jeune syndrome, NIK deficiency |
| PSEN2 | 2 / 21 | dilated cardiomyopathy 1V, Jeune 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 ⇵ |
|---|---|---|---|---|---|
| Intraflagellar transport | Reactome | 16 / 54 | 50.1× | 6.46e-24 | 1.03e-20 ✓ sig. |
| Hedgehog 'off' state | Reactome | 11 / 56 | 33.2× | 1.66e-14 | 4.92e-12 ✓ sig. |
| Activation of SMO | Reactome | 3 / 18 | 28.2× | 1.52e-4 | 3.14e-3 ✓ sig. |
| Noncanonical activation of NOTCH3 | Reactome | 2 / 8 | 42.3× | 9.43e-4 | 1.30e-2 ✓ sig. |
| Detoxification of Reactive Oxygen Species | Reactome | 3 / 34 | 14.9× | 1.04e-3 | 1.40e-2 ✓ sig. |
| Regulated proteolysis of p75NTR | Reactome | 2 / 11 | 30.8× | 1.83e-3 | 2.14e-2 ✓ sig. |
| Vasopressin-regulated water reabsorption | KEGG | 3 / 44 | 11.5× | 2.20e-3 | 2.45e-2 ✓ sig. |
| Anchoring of the basal body to the plasma membrane | Reactome | 4 / 98 | 6.9× | 2.67e-3 | 2.83e-2 ✓ sig. |
| Anchoring fibril formation | Reactome | 2 / 15 | 22.6× | 3.44e-3 | 3.40e-2 ✓ sig. |
| NRIF signals cell death from the nucleus | Reactome | 2 / 15 | 22.6× | 3.44e-3 | 3.40e-2 ✓ sig. |
| Hedgehog signaling pathway | KEGG | 3 / 56 | 9.1× | 4.39e-3 | 4.02e-2 ✓ sig. |
| Crosslinking of collagen fibrils | Reactome | 2 / 18 | 18.8× | 4.96e-3 | 4.37e-2 ✓ sig. |
| NOTCH3 Activation and Transmission of Signal to the Nucleus | Reactome | 2 / 19 | 17.8× | 5.52e-3 | 4.67e-2 ✓ sig. |
| Longevity regulating pathway - multiple species | KEGG | 3 / 62 | 8.2× | 5.84e-3 | 4.85e-2 ✓ sig. |
| Biosynthesis of EPA-derived SPMs | Reactome | 1 / 1 | 169× | 5.91e-3 | 4.89e-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 ⇵ |
|---|---|---|---|---|---|
| cilium assembly | GO:0060271 | 29 / 237 | 32.2× | 7.32e-37 | 6.40e-33 ✓ sig. |
| intraciliary retrograde transport | GO:0035721 | 12 / 14 | 226× | 3.07e-28 | 1.43e-24 ✓ sig. |
| intraciliary transport | GO:0042073 | 15 / 36 | 110× | 5.34e-28 | 2.42e-24 ✓ sig. |
| cell projection organization | GO:0030030 | 23 / 214 | 28.3× | 1.11e-27 | 4.83e-24 ✓ sig. |
| intraciliary anterograde transport | GO:0035720 | 10 / 19 | 139× | 2.91e-20 | 4.99e-17 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 12 / 57 | 55.4× | 2.10e-18 | 2.67e-15 ✓ sig. |
| smoothened signaling pathway | GO:0007224 | 11 / 94 | 30.8× | 5.71e-14 | 3.29e-11 ✓ sig. |
| regulation of smoothened signaling pathway | GO:0008589 | 7 / 29 | 63.5× | 1.23e-11 | 4.45e-9 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 7 / 57 | 32.3× | 1.92e-9 | 3.99e-7 ✓ sig. |
| negative regulation of keratinocyte proliferation | GO:0010839 | 5 / 24 | 54.8× | 2.76e-8 | 4.09e-6 ✓ sig. |
| regulation of cilium assembly | GO:1902017 | 6 / 52 | 30.4× | 4.30e-8 | 5.96e-6 ✓ sig. |
| positive regulation of smoothened signaling pathway | GO:0045880 | 5 / 39 | 33.7× | 3.57e-7 | 3.52e-5 ✓ sig. |
| protein localization to cilium | GO:0061512 | 5 / 44 | 29.9× | 6.64e-7 | 5.94e-5 ✓ sig. |
| determination of left/right symmetry | GO:0007368 | 6 / 83 | 19.0× | 7.27e-7 | 6.42e-5 ✓ sig. |
| protein processing | GO:0016485 | 6 / 95 | 16.6× | 1.61e-6 | 1.22e-4 ✓ sig. |