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 13
27
Diseases
254
Unique genes
0.085
Avg. similarity score
Ciliopathy
Most-connected disease (13 links)
Disease
Searched: Nephronophthisis 2
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Nephronophthisis 2
Ciliopathy
Joubert syndrome
Nephronophthisis
Aplasia of the vermis
Bardet-biedl syndrome
Senior-loken syndrome
Cystic kidney disease
Meckel-gruber syndrome
Orofaciodigital syndrome
Heart defect, tongue hamartoma and polysyndactyly
Joubert syndrome 24
Molar tooth sign
Nephronophthisis 4
Polydactyly
Alsahan-harris syndrome
Bardet-biedl syndrome 16
Cone-rod dystrophy 20
Mckusick-kaufman syndrome
Orofaciodigital syndrome type 14
ALG6-congenital disorder of glycosylation 1C
Hepatorenocardiac degenerative fibrosis
Morbid obesity and spermatogenic failure
Nephronophthisis 20
Nephronophthisis 7
Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy
Retinitis pigmentosa with or without situs inversus
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ciliopathy | 13 | 13 | 81 |
| Joubert syndrome | 13 | 13 | 61 |
| Nephronophthisis | 12 | 12 | 41 |
| Aplasia of the vermis | 11 | 11 | 54 |
| Bardet-biedl syndrome | 10 | 10 | 60 |
| Senior-loken syndrome | 7 | 7 | 13 |
| Cystic kidney disease | 6 | 6 | 32 |
| Meckel-gruber syndrome | 6 | 6 | 34 |
| Orofaciodigital syndrome | 6 | 6 | 34 |
| Heart defect, tongue hamartoma and polysyndactyly | 4 | 4 | 1 |
| Joubert syndrome 24 | 4 | 4 | 1 |
| Molar tooth sign | 4 | 4 | 1 |
| Nephronophthisis 4 | 4 | 4 | 1 |
| Polydactyly | 4 | 4 | 70 |
| Alsahan-harris syndrome | 3 | 3 | 1 |
| Bardet-biedl syndrome 16 | 3 | 3 | 1 |
| Nephronophthisis 2 | 3 | 3 | 1 |
| Cone-rod dystrophy 20 | 2 | 2 | 1 |
| Mckusick-kaufman syndrome | 2 | 2 | 1 |
| Orofaciodigital syndrome type 14 | 2 | 2 | 1 |
| ALG6-congenital disorder of glycosylation 1C | 1 | 1 | 1 |
| Hepatorenocardiac degenerative fibrosis | 1 | 1 | 1 |
| Morbid obesity and spermatogenic failure | 1 | 1 | 1 |
| Nephronophthisis 20 | 1 | 1 | 1 |
| Nephronophthisis 7 | 1 | 1 | 1 |
| Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy | 1 | 1 | 1 |
| Retinitis pigmentosa with or without situs inversus | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases ‐ top 100 shown, download for all)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CEP290 | 8 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 4 more |
| CC2D2A | 7 / 27 | Aplasia of the vermis, Ciliopathy, Cystic kidney disease, Joubert syndrome and 3 more |
| MKS1 | 7 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| RPGRIP1L | 7 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| TMEM67 | 7 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Cystic kidney disease and 3 more |
| NPHP3 | 6 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome and 2 more |
| RLIG1 | 6 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome and 2 more |
| SDCCAG8 | 6 / 27 | Bardet-biedl syndrome, Bardet-biedl syndrome 16, Ciliopathy, Cystic kidney disease and 2 more |
| TMEM216 | 6 / 27 | Aplasia of the vermis, Ciliopathy, Cystic kidney disease, Joubert syndrome and 2 more |
| WDPCP | 6 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Heart defect, tongue hamartoma and polysyndactyly and 2 more |
| CBY1 | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Molar tooth sign and 1 more |
| CPLANE1 | 5 / 27 | Aplasia of the vermis, Joubert syndrome, Nephronophthisis, Orofaciodigital syndrome and 1 more |
| KIF7 | 5 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Orofaciodigital syndrome and 1 more |
| NPHP1 | 5 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis and 1 more |
| NPHP4 | 5 / 27 | Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis, Nephronophthisis 4 and 1 more |
| OFD1 | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Orofaciodigital syndrome and 1 more |
| PDE6D | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Orofaciodigital syndrome and 1 more |
| TCTN2 | 5 / 27 | Aplasia of the vermis, Cystic kidney disease, Joubert syndrome, Joubert syndrome 24 and 1 more |
| TCTN3 | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome and 1 more |
| TMEM17 | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome and 1 more |
| TMEM231 | 5 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome and 1 more |
| B9D1 | 4 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| B9D2 | 4 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| IFT172 | 4 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Nephronophthisis |
| IFT74 | 4 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Ciliopathy, Joubert syndrome |
| INVS | 4 / 27 | Cystic kidney disease, Nephronophthisis, Nephronophthisis 2, Senior-loken syndrome |
| IQCB1 | 4 / 27 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| KIAA0586 | 4 / 27 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome, Polydactyly |
| MKKS | 4 / 27 | Bardet-biedl syndrome, Ciliopathy, Mckusick-kaufman syndrome, Nephronophthisis |
| SCLT1 | 4 / 27 | Bardet-biedl syndrome, Ciliopathy, Orofaciodigital syndrome, Senior-loken syndrome |
| TBC1D32 | 4 / 27 | Alsahan-harris syndrome, Ciliopathy, Joubert syndrome, Orofaciodigital syndrome |
| TMEM107 | 4 / 27 | Ciliopathy, Joubert syndrome, Meckel-gruber syndrome, Orofaciodigital syndrome |
| TMEM138 | 4 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| TMEM218 | 4 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome, Meckel-gruber syndrome |
| TTC21B | 4 / 27 | Aplasia of the vermis, Bardet-biedl syndrome, Joubert syndrome, Nephronophthisis |
| WDR19 | 4 / 27 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| AHI1 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Nephronophthisis |
| ARL6 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| BBS1 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| BBS10 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| BBS12 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| BBS9 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Nephronophthisis |
| C2CD3 | 3 / 27 | Aplasia of the vermis, Orofaciodigital syndrome, Orofaciodigital syndrome type 14 |
| CEP104 | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP120 | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP164 | 3 / 27 | Ciliopathy, Nephronophthisis, Senior-loken syndrome |
| CEP41 | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| CEP76 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Joubert syndrome |
| CSPP1 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome |
| DDX59 | 3 / 27 | Ciliopathy, Orofaciodigital syndrome, Polydactyly |
| FAM149B1 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Orofaciodigital syndrome |
| IFT140 | 3 / 27 | Joubert syndrome, Nephronophthisis, Orofaciodigital syndrome |
| IFT27 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| IFT57 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Orofaciodigital syndrome |
| KATNIP | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| KIAA0753 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Orofaciodigital syndrome |
| LZTFL1 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| PIBF1 | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| POC1B | 3 / 27 | Ciliopathy, Cone-rod dystrophy 20, Joubert syndrome |
| RPGRIP1 | 3 / 27 | Bardet-biedl syndrome, Joubert syndrome, Meckel-gruber syndrome |
| SUFU | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| TCTN1 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome |
| TMEM237 | 3 / 27 | Aplasia of the vermis, Joubert syndrome, Meckel-gruber syndrome |
| TOGARAM1 | 3 / 27 | Aplasia of the vermis, Ciliopathy, Joubert syndrome |
| TTC8 | 3 / 27 | Bardet-biedl syndrome, Ciliopathy, Polydactyly |
| ZNF423 | 3 / 27 | Ciliopathy, Joubert syndrome, Nephronophthisis |
| ADAMTS9 | 2 / 27 | Ciliopathy, Nephronophthisis |
| AKT3 | 2 / 27 | Bardet-biedl syndrome, Senior-loken syndrome |
| ALG6 | 2 / 27 | ALG6-congenital disorder of glycosylation 1C, Cystic kidney disease |
| ANKS6 | 2 / 27 | Cystic kidney disease, Nephronophthisis |
| ARL13B | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| ARL2BP | 2 / 27 | Ciliopathy, Retinitis pigmentosa with or without situs inversus |
| ARL3 | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| ARMC9 | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| ATP6V0A2 | 2 / 27 | Aplasia of the vermis, Meckel-gruber syndrome |
| BBIP1 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| BBS2 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| BBS4 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| BBS5 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| BBS7 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| CEP19 | 2 / 27 | Bardet-biedl syndrome, Morbid obesity and spermatogenic failure |
| CEP83 | 2 / 27 | Ciliopathy, Nephronophthisis |
| CFAP418 | 2 / 27 | Bardet-biedl syndrome, Ciliopathy |
| CIBAR1 | 2 / 27 | Ciliopathy, Polydactyly |
| DCDC2 | 2 / 27 | Ciliopathy, Nephronophthisis |
| DNAJB11 | 2 / 27 | Ciliopathy, Cystic kidney disease |
| EXOC8 | 2 / 27 | Aplasia of the vermis, Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy |
| GLI1 | 2 / 27 | Bardet-biedl syndrome, Polydactyly |
| GLI2 | 2 / 27 | Bardet-biedl syndrome, Polydactyly |
| GLIS2 | 2 / 27 | Nephronophthisis, Nephronophthisis 7 |
| HYLS1 | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| IFT43 | 2 / 27 | Ciliopathy, Polydactyly |
| IFT80 | 2 / 27 | Cystic kidney disease, Polydactyly |
| INPP5E | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| INTU | 2 / 27 | Nephronophthisis, Orofaciodigital syndrome |
| KIF14 | 2 / 27 | Joubert syndrome, Meckel-gruber syndrome |
| MAPKBP1 | 2 / 27 | Nephronophthisis, Nephronophthisis 20 |
| SLC30A7 | 2 / 27 | Aplasia of the vermis, Joubert syndrome |
| SMAD6 | 2 / 27 | Joubert syndrome, Polydactyly |
| TOPORS | 2 / 27 | Ciliopathy, Orofaciodigital 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 | 26 / 98 | 12.5× | 7.88e-22 | 8.20e-19 ✓ sig. |
| Hedgehog 'off' state | Reactome | 21 / 56 | 17.7× | 2.06e-21 | 1.95e-18 ✓ sig. |
| BBSome-mediated cargo-targeting to cilium | Reactome | 13 / 23 | 26.7× | 1.18e-16 | 4.90e-14 ✓ sig. |
| Intraflagellar transport | Reactome | 17 / 54 | 14.9× | 4.65e-16 | 1.76e-13 ✓ sig. |
| Hedgehog signaling pathway | KEGG | 14 / 56 | 11.8× | 6.59e-12 | 1.04e-9 ✓ sig. |
| Activation of SMO | Reactome | 7 / 18 | 18.4× | 4.55e-8 | 2.80e-6 ✓ sig. |
| Basal cell carcinoma | KEGG | 9 / 63 | 6.8× | 6.42e-6 | 2.02e-4 ✓ sig. |
| ARL13B-mediated ciliary trafficking of INPP5E | Reactome | 3 / 3 | 47.3× | 9.35e-6 | 2.75e-4 ✓ sig. |
| GLI proteins bind promoters of Hh responsive genes to promote transcription | Reactome | 3 / 3 | 47.3× | 9.35e-6 | 2.75e-4 ✓ sig. |
| Loss of Nlp from mitotic centrosomes | Reactome | 9 / 70 | 6.1× | 1.55e-5 | 4.21e-4 ✓ sig. |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 9 / 70 | 6.1× | 1.55e-5 | 4.21e-4 ✓ sig. |
| Hedgehog 'on' state | Reactome | 9 / 70 | 6.1× | 1.55e-5 | 4.21e-4 ✓ sig. |
| AURKA Activation by TPX2 | Reactome | 9 / 73 | 5.8× | 2.19e-5 | 5.62e-4 ✓ sig. |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 9 / 82 | 5.2× | 5.60e-5 | 1.19e-3 ✓ sig. |
| Regulation of PLK1 Activity at G2/M Transition | Reactome | 9 / 88 | 4.8× | 9.79e-5 | 1.86e-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 | 80 / 237 | 24.8× | 3.77e-92 | 4.78e-87 ✓ sig. |
| cell projection organization | GO:0030030 | 66 / 214 | 22.7× | 2.30e-72 | 1.75e-67 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 30 / 57 | 38.7× | 1.76e-41 | 2.16e-37 ✓ sig. |
| smoothened signaling pathway | GO:0007224 | 31 / 94 | 24.3× | 6.59e-35 | 5.02e-31 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 20 / 57 | 25.8× | 1.68e-23 | 4.36e-20 ✓ sig. |
| regulation of smoothened signaling pathway | GO:0008589 | 16 / 29 | 40.6× | 4.89e-23 | 1.18e-19 ✓ sig. |
| kidney development | GO:0001822 | 26 / 146 | 13.1× | 8.30e-22 | 1.74e-18 ✓ sig. |
| determination of left/right symmetry | GO:0007368 | 21 / 83 | 18.6× | 3.18e-21 | 6.26e-18 ✓ sig. |
| intraciliary transport | GO:0042073 | 16 / 36 | 32.7× | 4.84e-21 | 9.08e-18 ✓ sig. |
| positive regulation of smoothened signaling pathway | GO:0045880 | 15 / 39 | 28.3× | 1.24e-18 | 1.61e-15 ✓ sig. |
| protein localization to cilium | GO:0061512 | 14 / 44 | 23.4× | 4.10e-16 | 3.56e-13 ✓ sig. |
| fat cell differentiation | GO:0045444 | 16 / 93 | 12.7× | 1.27e-13 | 7.15e-11 ✓ sig. |
| neural tube patterning | GO:0021532 | 7 / 8 | 64.4× | 6.24e-13 | 3.05e-10 ✓ sig. |
| intraciliary anterograde transport | GO:0035720 | 9 / 19 | 34.8× | 1.13e-12 | 5.30e-10 ✓ sig. |
| heart looping | GO:0001947 | 13 / 64 | 14.9× | 2.82e-12 | 1.22e-9 ✓ sig. |