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 8
35
Diseases
235
Unique genes
0.074
Avg. similarity score
Ciliopathy
Most-connected disease (18 links)
Disease
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Ciliopathy
Aplasia of the vermis
Bardet-biedl syndrome
Joubert syndrome
Nephronophthisis
Cystic kidney disease
Senior-loken syndrome
Meckel-gruber syndrome
Orofaciodigital syndrome
Arima syndrome
Congenital cerebral hernia
Congenital cystic kidney disease
Dandy-walker syndrome
Heart defect, tongue hamartoma and polysyndactyly
joubert syndrome 21
joubert syndrome 24
nephronophthisis 4
BBS12-related ciliopathy
CEP164-related ciliopathy
Polydactyly
bardet-biedl syndrome 16
joubert syndrome 30
nephronophthisis 1
nephronophthisis 2
BBS1-related ciliopathy
BBS2-related ciliopathy
BBS4-related ciliopathy
BBS7-related ciliopathy
LZTFL1-related ciliopathy
MKKS-related ciliopathy
orofaciodigital syndrome type 14
ALG6-congenital disorder of glycosylation 1C
Retinitis pigmentosa with or without situs inversus
nephronophthisis 20
nephronophthisis 7
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CC2D2A | 8 / 35 | Aplasia of the vermis, Arima syndrome, Ciliopathy, Cystic kidney disease and 4 more |
| CEP290 | 8 / 35 | Aplasia of the vermis, Arima syndrome, Bardet-biedl syndrome, Cystic kidney disease and 4 more |
| MKS1 | 7 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| RPGRIP1L | 7 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| TMEM216 | 7 / 35 | Aplasia of the vermis, Arima syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| TMEM231 | 7 / 35 | Aplasia of the vermis, Arima syndrome, Ciliopathy, Congenital cystic kidney disease and 3 more |
| TMEM67 | 7 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| NPHP1 | 6 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis and 2 more |
| NPHP3 | 6 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome and 2 more |
| RLIG1 | 6 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome and 2 more |
| SDCCAG8 | 6 / 35 | Bardet-biedl syndrome, bardet-biedl syndrome 16, Ciliopathy, Cystic kidney disease and 2 more |
| B9D1 | 5 / 35 | Aplasia of the vermis, Ciliopathy, Congenital cystic kidney disease, Joubert syndrome and 1 more |
| CPLANE1 | 5 / 35 | Aplasia of the vermis, Joubert syndrome, Nephronophthisis, Orofaciodigital syndrome and 1 more |
| CSPP1 | 5 / 35 | Aplasia of the vermis, Dandy-walker syndrome, Joubert syndrome, joubert syndrome 21 and 1 more |
| KIF7 | 5 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Orofaciodigital syndrome and 1 more |
| NPHP4 | 5 / 35 | Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis, nephronophthisis 4 and 1 more |
| OFD1 | 5 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Orofaciodigital syndrome and 1 more |
| PIBF1 | 5 / 35 | Aplasia of the vermis, Ciliopathy, Congenital cerebral hernia, Dandy-walker syndrome and 1 more |
| TCTN2 | 5 / 35 | Aplasia of the vermis, Cystic kidney disease, Joubert syndrome, joubert syndrome 24 and 1 more |
| TCTN3 | 5 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome and 1 more |
| TMEM138 | 5 / 35 | Aplasia of the vermis, Arima syndrome, Ciliopathy, Joubert syndrome and 1 more |
| WDPCP | 5 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Heart defect, tongue hamartoma and polysyndactyly and 1 more |
| ARMC9 | 4 / 35 | Aplasia of the vermis, Dandy-walker syndrome, Joubert syndrome, joubert syndrome 30 |
| B9D2 | 4 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| BBS12 | 4 / 35 | Bardet-biedl syndrome, BBS12-related ciliopathy, Ciliopathy, Polydactyly |
| CEP164 | 4 / 35 | CEP164-related ciliopathy, Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| IFT172 | 4 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Nephronophthisis |
| IFT74 | 4 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Joubert syndrome |
| INVS | 4 / 35 | Cystic kidney disease, Nephronophthisis, nephronophthisis 2, Senior-loken syndrome |
| IQCB1 | 4 / 35 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| KIAA0586 | 4 / 35 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome, Polydactyly |
| PDE6D | 4 / 35 | Aplasia of the vermis, ciliopathy, Joubert syndrome, Orofaciodigital syndrome |
| SCLT1 | 4 / 35 | Bardet-biedl syndrome, Ciliopathy, Orofaciodigital syndrome, Senior-loken syndrome |
| TMEM107 | 4 / 35 | Ciliopathy, Joubert syndrome, Meckel-gruber syndrome, Orofaciodigital syndrome |
| TMEM218 | 4 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| TMEM237 | 4 / 35 | Aplasia of the vermis, Arima syndrome, Joubert syndrome, Meckel-gruber syndrome |
| TTC21B | 4 / 35 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis |
| WDR19 | 4 / 35 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| ZNF423 | 4 / 35 | Arima syndrome, Ciliopathy, Joubert syndrome, Nephronophthisis |
| AHI1 | 3 / 35 | Aplasia of the vermis, Joubert syndrome, Nephronophthisis |
| BBS1 | 3 / 35 | Bardet-biedl syndrome, BBS1-related ciliopathy, Ciliopathy |
| BBS10 | 3 / 35 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| BBS2 | 3 / 35 | Bardet-biedl syndrome, BBS2-related ciliopathy, Ciliopathy |
| BBS4 | 3 / 35 | Bardet-biedl syndrome, BBS4-related ciliopathy, Ciliopathy |
| BBS7 | 3 / 35 | Bardet-biedl syndrome, BBS7-related ciliopathy, Ciliopathy |
| BBS9 | 3 / 35 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis |
| C2CD3 | 3 / 35 | Aplasia of the vermis, Orofaciodigital syndrome, orofaciodigital syndrome type 14 |
| CBY1 | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP104 | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP120 | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP41 | 3 / 35 | Aplasia of the vermis, ciliopathy, Joubert syndrome |
| FAM149B1 | 3 / 35 | Aplasia of the vermis, Joubert syndrome, Orofaciodigital syndrome |
| HYLS1 | 3 / 35 | Aplasia of the vermis, Dandy-walker syndrome, Joubert syndrome |
| IFT140 | 3 / 35 | Joubert syndrome, Nephronophthisis, Orofaciodigital syndrome |
| IFT57 | 3 / 35 | Bardet-biedl syndrome, ciliopathy, Orofaciodigital syndrome |
| KATNIP | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| KIAA0753 | 3 / 35 | Aplasia of the vermis, Joubert syndrome, Orofaciodigital syndrome |
| KIF14 | 3 / 35 | Congenital cystic kidney disease, Joubert syndrome, Meckel-gruber syndrome |
| LZTFL1 | 3 / 35 | Bardet-biedl syndrome, Ciliopathy, LZTFL1-related ciliopathy |
| MKKS | 3 / 35 | Bardet-biedl syndrome, MKKS-related ciliopathy, Nephronophthisis |
| RPGRIP1 | 3 / 35 | Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome |
| SUFU | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| TBC1D32 | 3 / 35 | Ciliopathy, Joubert syndrome, Orofaciodigital syndrome |
| TCTN1 | 3 / 35 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome |
| TMEM17 | 3 / 35 | Aplasia of the vermis, Meckel-gruber syndrome, Orofaciodigital syndrome |
| TOGARAM1 | 3 / 35 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| TXNDC15 | 3 / 35 | Ciliopathy, Congenital cystic kidney disease, Meckel-gruber syndrome |
| ADAMTS9 | 2 / 35 | Ciliopathy, Nephronophthisis |
| AKT3 | 2 / 35 | Bardet-biedl syndrome, Senior-loken syndrome |
| ALG6 | 2 / 35 | ALG6-congenital disorder of glycosylation 1C, Cystic kidney disease |
| ANKS6 | 2 / 35 | Cystic kidney disease, Nephronophthisis |
| ARL13B | 2 / 35 | Aplasia of the vermis, Joubert syndrome |
| ARL2BP | 2 / 35 | Ciliopathy, Retinitis pigmentosa with or without situs inversus |
| ARL3 | 2 / 35 | Aplasia of the vermis, Joubert syndrome |
| ARL6 | 2 / 35 | Bardet-biedl syndrome, Ciliopathy |
| ATP6V0A2 | 2 / 35 | Aplasia of the vermis, Meckel-gruber syndrome |
| BBIP1 | 2 / 35 | Bardet-biedl syndrome, ciliopathy |
| CEP83 | 2 / 35 | Ciliopathy, Nephronophthisis |
| CFAP418 | 2 / 35 | Bardet-biedl syndrome, Ciliopathy |
| CIBAR1 | 2 / 35 | Ciliopathy, Polydactyly |
| DCDC2 | 2 / 35 | Ciliopathy, Nephronophthisis |
| DDX59 | 2 / 35 | ciliopathy, Orofaciodigital syndrome |
| GLI1 | 2 / 35 | Bardet-biedl syndrome, Polydactyly |
| GLIS2 | 2 / 35 | Nephronophthisis, nephronophthisis 7 |
| IFT27 | 2 / 35 | Bardet-biedl syndrome, Ciliopathy |
| IFT80 | 2 / 35 | Cystic kidney disease, Polydactyly |
| INPP5E | 2 / 35 | Aplasia of the vermis, Joubert syndrome |
| INTU | 2 / 35 | Nephronophthisis, Orofaciodigital syndrome |
| MAPKBP1 | 2 / 35 | Nephronophthisis, nephronophthisis 20 |
| SLC30A7 | 2 / 35 | Aplasia of the vermis, Joubert syndrome |
| SMAD6 | 2 / 35 | Joubert syndrome, Polydactyly |
| TOPORS | 2 / 35 | Ciliopathy, Orofaciodigital syndrome |
| TRAF3IP1 | 2 / 35 | Ciliopathy, Senior-loken syndrome |
| TTC8 | 2 / 35 | Bardet-biedl syndrome, Polydactyly |
| USH2A | 2 / 35 | Aplasia of the vermis, Bardet-biedl 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 ⇵ |
|---|---|---|---|---|---|
| Anchoring of the basal body to the plasma membrane | Reactome | 25 / 98 | 13.0× | 2.08e-21 | 2.11e-18 ✓ sig. |
| Hedgehog 'off' state | Reactome | 20 / 56 | 18.3× | 1.26e-20 | 1.09e-17 ✓ sig. |
| BBSome-mediated cargo-targeting to cilium | Reactome | 13 / 23 | 28.9× | 4.26e-17 | 2.04e-14 ✓ sig. |
| Intraflagellar transport | Reactome | 17 / 54 | 16.1× | 1.25e-16 | 5.54e-14 ✓ sig. |
| Hedgehog signaling pathway | KEGG | 14 / 56 | 12.8× | 2.29e-12 | 4.69e-10 ✓ sig. |
| Activation of SMO | Reactome | 7 / 18 | 19.9× | 2.66e-8 | 2.07e-6 ✓ sig. |
| ARL13B-mediated ciliary trafficking of INPP5E | Reactome | 3 / 3 | 51.1× | 7.40e-6 | 2.61e-4 ✓ sig. |
| GLI proteins bind promoters of Hh responsive genes to promote transcription | Reactome | 3 / 3 | 51.1× | 7.40e-6 | 2.61e-4 ✓ sig. |
| Hedgehog 'on' state | Reactome | 9 / 70 | 6.6× | 8.31e-6 | 2.87e-4 ✓ sig. |
| Basal cell carcinoma | KEGG | 8 / 63 | 6.5× | 2.92e-5 | 8.16e-4 ✓ sig. |
| Regulation of PLK1 Activity at G2/M Transition | Reactome | 9 / 88 | 5.2× | 5.38e-5 | 1.36e-3 ✓ sig. |
| Loss of Nlp from mitotic centrosomes | Reactome | 8 / 70 | 5.8× | 6.33e-5 | 1.55e-3 ✓ sig. |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 8 / 70 | 5.8× | 6.33e-5 | 1.55e-3 ✓ sig. |
| AURKA Activation by TPX2 | Reactome | 8 / 73 | 5.6× | 8.57e-5 | 1.98e-3 ✓ sig. |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 8 / 82 | 5.0× | 1.95e-4 | 3.84e-3 ✓ 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 | 77 / 237 | 25.8× | 4.67e-90 | 5.45e-85 ✓ sig. |
| cell projection organization | GO:0030030 | 64 / 214 | 23.8× | 1.52e-71 | 1.33e-66 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 29 / 57 | 40.5× | 1.44e-40 | 1.53e-36 ✓ sig. |
| smoothened signaling pathway | GO:0007224 | 31 / 94 | 26.2× | 5.36e-36 | 4.26e-32 ✓ sig. |
| regulation of smoothened signaling pathway | GO:0008589 | 16 / 29 | 43.9× | 1.37e-23 | 3.78e-20 ✓ sig. |
| determination of left/right symmetry | GO:0007368 | 20 / 83 | 19.2× | 1.76e-20 | 3.12e-17 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 17 / 57 | 23.7× | 2.45e-19 | 3.61e-16 ✓ sig. |
| positive regulation of smoothened signaling pathway | GO:0045880 | 14 / 39 | 28.5× | 1.91e-17 | 2.13e-14 ✓ sig. |
| kidney development | GO:0001822 | 21 / 146 | 11.4× | 1.53e-16 | 1.38e-13 ✓ sig. |
| intraciliary transport | GO:0042073 | 13 / 36 | 28.7× | 2.52e-16 | 2.21e-13 ✓ sig. |
| protein localization to cilium | GO:0061512 | 13 / 44 | 23.5× | 5.19e-15 | 3.54e-12 ✓ sig. |
| neural tube patterning | GO:0021532 | 7 / 8 | 69.6× | 3.60e-13 | 1.79e-10 ✓ sig. |
| intraciliary anterograde transport | GO:0035720 | 9 / 19 | 37.7× | 5.59e-13 | 2.70e-10 ✓ sig. |
| fat cell differentiation | GO:0045444 | 15 / 93 | 12.8× | 6.51e-13 | 3.09e-10 ✓ sig. |
| heart looping | GO:0001947 | 13 / 64 | 16.2× | 1.05e-12 | 4.82e-10 ✓ sig. |