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 7
35
Diseases
465
Unique genes
0.057
Avg. similarity score
Retinitis pigmentosa
Most-connected disease (20 links)
Disease
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Retinitis pigmentosa
Optic atrophy
Leber congenital amaurosis
Cone-rod dystrophy
Cone dystrophy
Macular dystrophy
Stargardt disease
Retinal degeneration
retinitis pigmentosa 65
CERKL-related retinopathy
PCARE-related retinopathy
RAB28-related retinopathy
cone-rod dystrophy 2
CNGA1-related retinopathy
Nystagmus
PHARC syndrome
BBS5-related ciliopathy
IDH3B-related retinopathy
PRPF31-related retinopathy
SNRNP200-related dominant retinopathy
TUBB4B-related ciliopathy
autosomal recessive optic atrophy, OPA7 type
leber congenital amaurosis 15
ornithine aminotransferase deficiency
retinitis pigmentosa 27
retinitis pigmentosa 86
retinitis pigmentosa 9
Alzahrani-kuwahara syndrome
Corneal degeneration
PDE6G-related retinopathy
Uridine-cytidineuria
foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome
macular corneal dystrophy
optic atrophy 11
optic atrophy 15
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases ‐ top 100 shown, download for all)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CNGB3 | 8 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 4 more |
| ABCA4 | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| CDHR1 | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| CRB1 | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| CRX | 7 / 35 | Cone-rod dystrophy, cone-rod dystrophy 2, Leber congenital amaurosis, Macular dystrophy and 3 more |
| GUCY2D | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| NMNAT1 | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus and 3 more |
| PRPH2 | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| RDH12 | 7 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Optic atrophy and 3 more |
| RHO | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Nystagmus, Optic atrophy and 3 more |
| RPGR | 7 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| CERKL | 6 / 35 | CERKL-related retinopathy, Cone dystrophy, Cone-rod dystrophy, Macular dystrophy and 2 more |
| GPHN | 6 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Optic atrophy and 2 more |
| KCNV2 | 6 / 35 | Cone dystrophy, Cone-rod dystrophy, Nystagmus, Optic atrophy and 2 more |
| PDE6B | 6 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 2 more |
| PROM1 | 6 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Optic atrophy and 2 more |
| RPE65 | 6 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus, Retinal degeneration and 2 more |
| RPGRIP1 | 6 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus and 2 more |
| USH2A | 6 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 2 more |
| CACNA1F | 5 / 35 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Optic atrophy and 1 more |
| CEP290 | 5 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus, Optic atrophy and 1 more |
| CNGA1 | 5 / 35 | CNGA1-related retinopathy, Cone-rod dystrophy, Macular dystrophy, Optic atrophy and 1 more |
| CNGA3 | 5 / 35 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Optic atrophy and 1 more |
| EYS | 5 / 35 | Cone-rod dystrophy, Macular dystrophy, Optic atrophy, Retinitis pigmentosa and 1 more |
| MFSD8 | 5 / 35 | Cone-rod dystrophy, Macular dystrophy, Optic atrophy, Retinitis pigmentosa and 1 more |
| OTX2 | 5 / 35 | Leber congenital amaurosis, Macular dystrophy, Nystagmus, Optic atrophy and 1 more |
| PCARE | 5 / 35 | Cone-rod dystrophy, Optic atrophy, PCARE-related retinopathy, Retinitis pigmentosa and 1 more |
| RAB28 | 5 / 35 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, RAB28-related retinopathy and 1 more |
| ABHD12 | 4 / 35 | Cone dystrophy, Optic atrophy, PHARC syndrome, Retinitis pigmentosa |
| AHI1 | 4 / 35 | Leber congenital amaurosis, Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| ALMS1 | 4 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| ATF6 | 4 / 35 | Cone-rod dystrophy, Macular dystrophy, Nystagmus, Retinitis pigmentosa |
| CABP4 | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| CACNA2D4 | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| CFAP410 | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Retinitis pigmentosa |
| GUCA1A | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| GUCA1ANB-GUCA1A | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| GUCA1B | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Retinitis pigmentosa |
| LCA5 | 4 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| MKS1 | 4 / 35 | Leber congenital amaurosis, Nystagmus, Optic atrophy, Retinitis pigmentosa |
| NR2E3 | 4 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| OPA1 | 4 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| PANK2 | 4 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| PDE6C | 4 / 35 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| RP2 | 4 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Retinitis pigmentosa |
| RPGRIP1L | 4 / 35 | Leber congenital amaurosis, Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| SCLT1 | 4 / 35 | Cone-rod dystrophy, Nystagmus, Optic atrophy, Retinitis pigmentosa |
| SPATA7 | 4 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| TULP1 | 4 / 35 | Leber congenital amaurosis, leber congenital amaurosis 15, Retinitis pigmentosa, Stargardt disease |
| WDR19 | 4 / 35 | Cone dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| AIPL1 | 3 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Retinitis pigmentosa |
| ARL6 | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| BBS5 | 3 / 35 | BBS5-related ciliopathy, Cone dystrophy, Retinitis pigmentosa |
| BEST1 | 3 / 35 | Macular dystrophy, Retinitis pigmentosa, Stargardt disease |
| CEP78 | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| CFH | 3 / 35 | Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| COL18A1 | 3 / 35 | Macular dystrophy, Nystagmus, Retinitis pigmentosa |
| COL2A1 | 3 / 35 | Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| DTHD1 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| EFEMP1 | 3 / 35 | Macular dystrophy, Optic atrophy, Retinitis pigmentosa |
| GRM6 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| IDH3B | 3 / 35 | IDH3B-related retinopathy, Optic atrophy, Retinitis pigmentosa |
| IFT140 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| IMPG1 | 3 / 35 | Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| IMPG2 | 3 / 35 | Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| INPP5E | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| KIAA1549 | 3 / 35 | Optic atrophy, Retinitis pigmentosa, retinitis pigmentosa 86 |
| LRAT | 3 / 35 | Leber congenital amaurosis, Retinitis pigmentosa, Stargardt disease |
| LRIT3 | 3 / 35 | Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| LRP5 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| MERTK | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| MYO7A | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NBAS | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NPHP3 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NPHP4 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NRL | 3 / 35 | Retinal degeneration, Retinitis pigmentosa, retinitis pigmentosa 27 |
| OAT | 3 / 35 | Optic atrophy, ornithine aminotransferase deficiency, Retinitis pigmentosa |
| PCDH15 | 3 / 35 | Cone dystrophy, Optic atrophy, Retinitis pigmentosa |
| PITPNM3 | 3 / 35 | Cone dystrophy, Cone-rod dystrophy, Retinitis pigmentosa |
| PRPF31 | 3 / 35 | Leber congenital amaurosis, PRPF31-related retinopathy, Retinitis pigmentosa |
| RAX2 | 3 / 35 | Cone-rod dystrophy, Retinal degeneration, Retinitis pigmentosa |
| RBP3 | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| RGR | 3 / 35 | Cone dystrophy, Optic atrophy, Retinitis pigmentosa |
| RGS9 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| RIMS1 | 3 / 35 | Cone-rod dystrophy, Leber congenital amaurosis, Retinitis pigmentosa |
| ROM1 | 3 / 35 | Macular dystrophy, Optic atrophy, Retinitis pigmentosa |
| RP1 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| RP1L1 | 3 / 35 | Cone dystrophy, Optic atrophy, Retinitis pigmentosa |
| RP9 | 3 / 35 | Optic atrophy, Retinitis pigmentosa, retinitis pigmentosa 9 |
| SEMA4A | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| SLC19A1 | 3 / 35 | Macular dystrophy, Nystagmus, Retinitis pigmentosa |
| SNRNP200 | 3 / 35 | Retinitis pigmentosa, SNRNP200-related dominant retinopathy, Stargardt disease |
| TMEM126A | 3 / 35 | autosomal recessive optic atrophy, OPA7 type, Optic atrophy, Retinitis pigmentosa |
| TOPORS | 3 / 35 | Macular dystrophy, Optic atrophy, Retinitis pigmentosa |
| TTC8 | 3 / 35 | Leber congenital amaurosis, Macular dystrophy, Retinitis pigmentosa |
| TTLL5 | 3 / 35 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| TUBB4B | 3 / 35 | Leber congenital amaurosis, Retinitis pigmentosa, TUBB4B-related ciliopathy |
| UNC119 | 3 / 35 | Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| USP45 | 3 / 35 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| ZFYVE26 | 3 / 35 | Leber congenital amaurosis, Macular dystrophy, Retinitis pigmentosa |
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 ⇵ |
|---|---|---|---|---|---|
| Phototransduction | KEGG | 17 / 29 | 15.1× | 2.51e-17 | 1.25e-14 ✓ sig. |
| BBSome-mediated cargo-targeting to cilium | Reactome | 14 / 23 | 15.7× | 8.34e-15 | 2.65e-12 ✓ sig. |
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 13 / 20 | 16.8× | 2.26e-14 | 6.52e-12 ✓ sig. |
| Inactivation, recovery and regulation of the phototransduction cascade | Reactome | 14 / 33 | 11.0× | 5.85e-12 | 1.10e-9 ✓ sig. |
| Activation of the phototransduction cascade | Reactome | 8 / 9 | 23.0× | 4.14e-11 | 6.51e-9 ✓ sig. |
| Retinoid cycle disease events | Reactome | 9 / 13 | 17.9× | 1.13e-10 | 1.61e-8 ✓ sig. |
| Anchoring of the basal body to the plasma membrane | Reactome | 21 / 98 | 5.5× | 1.14e-10 | 1.61e-8 ✓ sig. |
| Intraflagellar transport | Reactome | 15 / 54 | 7.2× | 1.13e-9 | 1.26e-7 ✓ sig. |
| Hedgehog 'off' state | Reactome | 11 / 56 | 5.1× | 8.00e-6 | 2.78e-4 ✓ sig. |
| Recruitment of NuMA to mitotic centrosomes | Reactome | 14 / 94 | 3.8× | 1.42e-5 | 4.50e-4 ✓ sig. |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 13 / 82 | 4.1× | 1.44e-5 | 4.54e-4 ✓ sig. |
| Loss of Nlp from mitotic centrosomes | Reactome | 11 / 70 | 4.1× | 7.13e-5 | 1.70e-3 ✓ sig. |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 11 / 70 | 4.1× | 7.13e-5 | 1.70e-3 ✓ sig. |
| AURKA Activation by TPX2 | Reactome | 11 / 73 | 3.9× | 1.06e-4 | 2.36e-3 ✓ sig. |
| The retinoid cycle in cones (daylight vision) | Reactome | 4 / 8 | 12.9× | 1.37e-4 | 2.89e-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 ⇵ |
|---|---|---|---|---|---|
| visual perception | GO:0007601 | 115 / 215 | 21.5× | 2.48e-129 | 8.67e-124 ✓ sig. |
| photoreceptor cell maintenance | GO:0045494 | 35 / 45 | 31.3× | 5.08e-48 | 8.89e-44 ✓ sig. |
| retina development in camera-type eye | GO:0060041 | 40 / 85 | 18.9× | 1.33e-41 | 1.67e-37 ✓ sig. |
| cilium assembly | GO:0060271 | 54 / 237 | 9.2× | 2.00e-36 | 1.67e-32 ✓ sig. |
| cell projection organization | GO:0030030 | 44 / 214 | 8.3× | 8.40e-28 | 3.72e-24 ✓ sig. |
| detection of light stimulus involved in visual perception | GO:0050908 | 17 / 24 | 28.5× | 1.19e-22 | 2.79e-19 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 23 / 57 | 16.2× | 1.81e-22 | 4.22e-19 ✓ sig. |
| photoreceptor cell outer segment organization | GO:0035845 | 13 / 15 | 34.8× | 1.19e-19 | 1.84e-16 ✓ sig. |
| sensory perception of light stimulus | GO:0050953 | 12 / 13 | 37.1× | 6.23e-19 | 8.55e-16 ✓ sig. |
| intraciliary transport | GO:0042073 | 15 / 36 | 16.7× | 2.40e-15 | 1.75e-12 ✓ sig. |
| retina homeostasis | GO:0001895 | 11 / 15 | 29.5× | 2.52e-15 | 1.84e-12 ✓ sig. |
| eye photoreceptor cell development | GO:0042462 | 12 / 21 | 23.0× | 1.18e-14 | 7.56e-12 ✓ sig. |
| phototransduction | GO:0007602 | 13 / 34 | 15.4× | 6.85e-13 | 3.25e-10 ✓ sig. |
| retina layer formation | GO:0010842 | 11 / 27 | 16.4× | 1.83e-11 | 6.33e-9 ✓ sig. |
| camera-type eye development | GO:0043010 | 16 / 74 | 8.7× | 2.99e-11 | 9.70e-9 ✓ sig. |