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 10
29
Diseases
567
Unique genes
0.077
Avg. similarity score
Leber congenital amaurosis
Most-connected disease (14 links)
Disease
Searched: Macular dystrophy with or without cone dysfunction
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Macular dystrophy with or without cone dysfunction
Leber congenital amaurosis
Cone-rod dystrophy
Macular dystrophy
Optic atrophy
Stargardt disease
Cone dystrophy
Retinitis pigmentosa
Retinopathy
Eye disorders
Retinal degeneration
Retinitis pigmentosa 65
Cone-rod dystrophy 2
Macular dystrophy with central cone involvement
Retinal detachment
X-linked retinitis pigmentosa
Achromatopsia
Nystagmus
Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facies
Leber congenital amaurosis 15
Retinitis pigmentosa 27
Retinitis pigmentosa 9
Spastic paraplegia 15, autosomal recessive
Corneal degeneration
Macular corneal dystrophy
Multiple mitochondrial dysfunctions syndrome 4
Optic atrophy 11
Uridine-cytidineuria
Yuksel-vogel-bauer syndrome
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 | 10 / 29 | Achromatopsia, Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis and 6 more |
| ABCA4 | 9 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 5 more |
| CRB1 | 9 / 29 | Cone dystrophy, Cone-rod dystrophy, Eye disorders, Leber congenital amaurosis and 5 more |
| RHO | 9 / 29 | Cone dystrophy, Cone-rod dystrophy, Nystagmus, Optic atrophy and 5 more |
| CNGA3 | 8 / 29 | Achromatopsia, Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis and 4 more |
| NMNAT1 | 8 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus and 4 more |
| PRPH2 | 8 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 4 more |
| RDH12 | 8 / 29 | Cone-rod dystrophy, Eye disorders, Leber congenital amaurosis, Macular dystrophy and 4 more |
| RPGR | 8 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 4 more |
| CDHR1 | 7 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| CRX | 7 / 29 | Cone-rod dystrophy, Cone-rod dystrophy 2, Leber congenital amaurosis, Macular dystrophy and 3 more |
| EYS | 7 / 29 | Cone-rod dystrophy, Macular dystrophy, Optic atrophy, Retinal detachment and 3 more |
| GUCY2D | 7 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 3 more |
| MFSD8 | 7 / 29 | Cone-rod dystrophy, Eye disorders, Macular dystrophy, Macular dystrophy with central cone involvement and 3 more |
| RPE65 | 7 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus, Retinal degeneration and 3 more |
| ATF6 | 6 / 29 | Achromatopsia, Cone-rod dystrophy, Macular dystrophy, Nystagmus and 2 more |
| CACNA1F | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Optic atrophy and 2 more |
| CEP290 | 6 / 29 | Cone-rod dystrophy, Eye disorders, Leber congenital amaurosis, Nystagmus and 2 more |
| CERKL | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa and 2 more |
| GPHN | 6 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Optic atrophy and 2 more |
| KCNV2 | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Nystagmus, Optic atrophy and 2 more |
| PDE6B | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 2 more |
| PDE6C | 6 / 29 | Achromatopsia, Cone dystrophy, Cone-rod dystrophy, Optic atrophy and 2 more |
| PROM1 | 6 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Optic atrophy and 2 more |
| RP2 | 6 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy, Retinitis pigmentosa and 2 more |
| RPGRIP1 | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Nystagmus and 2 more |
| USH2A | 6 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Macular dystrophy and 2 more |
| AIPL1 | 5 / 29 | Cone-rod dystrophy, Eye disorders, Leber congenital amaurosis, Retinitis pigmentosa and 1 more |
| CACNA2D4 | 5 / 29 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa and 1 more |
| CFH | 5 / 29 | Optic atrophy, Retinal degeneration, Retinal detachment, Retinitis pigmentosa and 1 more |
| CNGA1 | 5 / 29 | Cone-rod dystrophy, Macular dystrophy, Optic atrophy, Retinitis pigmentosa and 1 more |
| COL2A1 | 5 / 29 | Eye disorders, Optic atrophy, Retinal detachment, Retinitis pigmentosa and 1 more |
| GUCA1B | 5 / 29 | Cone dystrophy, Cone-rod dystrophy, Eye disorders, Leber congenital amaurosis and 1 more |
| LCA5 | 5 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa, Retinopathy and 1 more |
| OTX2 | 5 / 29 | Leber congenital amaurosis, Macular dystrophy, Nystagmus, Optic atrophy and 1 more |
| PCARE | 5 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Retinopathy and 1 more |
| RAB28 | 5 / 29 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa and 1 more |
| RP1 | 5 / 29 | Eye disorders, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa and 1 more |
| RPGRIP1L | 5 / 29 | Eye disorders, Leber congenital amaurosis, Optic atrophy, Retinal degeneration and 1 more |
| ABHD12 | 4 / 29 | Cone dystrophy, Nystagmus, Optic atrophy, Retinitis pigmentosa |
| AHI1 | 4 / 29 | Leber congenital amaurosis, Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| ALMS1 | 4 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| CABP4 | 4 / 29 | Cone dystrophy, Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| CFAP410 | 4 / 29 | Cone dystrophy, Cone-rod dystrophy, Leber congenital amaurosis, Retinitis pigmentosa |
| DRAM2 | 4 / 29 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| GNAT2 | 4 / 29 | Achromatopsia, Cone dystrophy, Retinitis pigmentosa, Retinopathy |
| GRM6 | 4 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa, Retinopathy |
| GUCA1A | 4 / 29 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| GUCA1ANB-GUCA1A | 4 / 29 | Cone dystrophy, Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| LRP5 | 4 / 29 | Eye disorders, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| MERTK | 4 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Retinopathy |
| MKS1 | 4 / 29 | Leber congenital amaurosis, Nystagmus, Optic atrophy, Retinitis pigmentosa |
| NDP | 4 / 29 | Eye disorders, Nystagmus, Retinal detachment, Retinitis pigmentosa |
| NR2E3 | 4 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| OPA1 | 4 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| PANK2 | 4 / 29 | Cone-rod dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| RDH5 | 4 / 29 | Optic atrophy, Retinal detachment, Retinitis pigmentosa, Retinopathy |
| RLBP1 | 4 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Retinopathy |
| SCLT1 | 4 / 29 | Cone-rod dystrophy, Nystagmus, Optic atrophy, Retinitis pigmentosa |
| SEMA4A | 4 / 29 | Cone-rod dystrophy, Eye disorders, Optic atrophy, Retinitis pigmentosa |
| SPATA7 | 4 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| TOPORS | 4 / 29 | Macular dystrophy, Optic atrophy, Retinitis pigmentosa, Retinopathy |
| TTLL5 | 4 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa, Retinopathy |
| TULP1 | 4 / 29 | Leber congenital amaurosis, Leber congenital amaurosis 15, Retinitis pigmentosa, Stargardt disease |
| WDR19 | 4 / 29 | Cone dystrophy, Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| ZFYVE26 | 4 / 29 | Leber congenital amaurosis, Macular dystrophy, Retinitis pigmentosa, Spastic paraplegia 15, autosomal recessive |
| ACO2 | 3 / 29 | Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| ADAM9 | 3 / 29 | Cone-rod dystrophy, Retinitis pigmentosa, Retinopathy |
| ARL3 | 3 / 29 | Cone dystrophy, Cone-rod dystrophy, Retinitis pigmentosa |
| ARL6 | 3 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| BEST1 | 3 / 29 | Macular dystrophy, Retinitis pigmentosa, Stargardt disease |
| C1QTNF5 | 3 / 29 | Optic atrophy, Retinal degeneration, Retinitis pigmentosa |
| CEP78 | 3 / 29 | Cone-rod dystrophy, Optic atrophy, Retinitis pigmentosa |
| CNGB1 | 3 / 29 | Optic atrophy, Retinitis pigmentosa, Retinopathy |
| COL18A1 | 3 / 29 | Macular dystrophy, Nystagmus, Retinitis pigmentosa |
| COL22A1 | 3 / 29 | Retinal degeneration, Retinal detachment, Retinopathy |
| DTHD1 | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| EFEMP1 | 3 / 29 | Macular dystrophy, Optic atrophy, Retinitis pigmentosa |
| ELOVL1 | 3 / 29 | Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facies, Optic atrophy, Retinitis pigmentosa |
| GPR179 | 3 / 29 | Optic atrophy, Retinitis pigmentosa, Retinopathy |
| IDH3B | 3 / 29 | Optic atrophy, Retinitis pigmentosa, Retinopathy |
| IFT140 | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| IMPDH1 | 3 / 29 | Leber congenital amaurosis, Retinitis pigmentosa, Retinopathy |
| IMPG1 | 3 / 29 | Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| IMPG2 | 3 / 29 | Cone-rod dystrophy, Macular dystrophy, Retinitis pigmentosa |
| INPP5E | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| LRAT | 3 / 29 | Leber congenital amaurosis, Retinitis pigmentosa, Stargardt disease |
| LRIT3 | 3 / 29 | Optic atrophy, Retinitis pigmentosa, Stargardt disease |
| MAK | 3 / 29 | Eye disorders, Retinitis pigmentosa, Retinopathy |
| MYO7A | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NBAS | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NPHP1 | 3 / 29 | Eye disorders, Leber congenital amaurosis, Retinitis pigmentosa |
| NPHP3 | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NPHP4 | 3 / 29 | Leber congenital amaurosis, Optic atrophy, Retinitis pigmentosa |
| NRL | 3 / 29 | Retinal degeneration, Retinitis pigmentosa, Retinitis pigmentosa 27 |
| PCDH15 | 3 / 29 | Cone dystrophy, Optic atrophy, Retinitis pigmentosa |
| PDE6A | 3 / 29 | Leber congenital amaurosis, Retinitis pigmentosa, Retinopathy |
| PDE6H | 3 / 29 | Achromatopsia, Cone dystrophy, Retinitis pigmentosa |
| PITPNM3 | 3 / 29 | Cone dystrophy, Cone-rod dystrophy, Retinitis pigmentosa |
| PRPF31 | 3 / 29 | Leber congenital amaurosis, Retinitis pigmentosa, Retinopathy |
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 | 12.4× | 6.96e-16 | 2.49e-13 ✓ sig. |
| BBSome-mediated cargo-targeting to cilium | Reactome | 14 / 23 | 12.9× | 1.29e-13 | 2.93e-11 ✓ sig. |
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 13 / 20 | 13.8× | 2.89e-13 | 6.08e-11 ✓ sig. |
| Inactivation, recovery and regulation of the phototransduction cascade | Reactome | 14 / 33 | 9.0× | 8.32e-11 | 9.97e-9 ✓ sig. |
| Activation of the phototransduction cascade | Reactome | 8 / 9 | 18.8× | 2.03e-10 | 2.20e-8 ✓ sig. |
| Retinoid cycle disease events | Reactome | 9 / 13 | 14.7× | 6.61e-10 | 6.43e-8 ✓ sig. |
| Anchoring of the basal body to the plasma membrane | Reactome | 22 / 98 | 4.8× | 6.91e-10 | 6.66e-8 ✓ sig. |
| Intraflagellar transport | Reactome | 15 / 54 | 5.9× | 1.68e-8 | 1.17e-6 ✓ sig. |
| Collagen biosynthesis and modifying enzymes | Reactome | 13 / 67 | 4.1× | 1.22e-5 | 3.43e-4 ✓ sig. |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 14 / 82 | 3.6× | 2.63e-5 | 6.53e-4 ✓ sig. |
| Recruitment of NuMA to mitotic centrosomes | Reactome | 15 / 94 | 3.4× | 3.13e-5 | 7.52e-4 ✓ sig. |
| Hedgehog 'off' state | Reactome | 11 / 56 | 4.2× | 5.05e-5 | 1.10e-3 ✓ sig. |
| Loss of Nlp from mitotic centrosomes | Reactome | 12 / 70 | 3.6× | 9.43e-5 | 1.81e-3 ✓ sig. |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 12 / 70 | 3.6× | 9.43e-5 | 1.81e-3 ✓ sig. |
| AURKA Activation by TPX2 | Reactome | 12 / 73 | 3.5× | 1.43e-4 | 2.52e-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 | 116 / 215 | 17.8× | 4.91e-120 | 1.87e-114 ✓ sig. |
| photoreceptor cell maintenance | GO:0045494 | 35 / 45 | 25.6× | 6.34e-45 | 1.05e-40 ✓ sig. |
| retina development in camera-type eye | GO:0060041 | 40 / 85 | 15.5× | 4.00e-38 | 4.22e-34 ✓ sig. |
| cilium assembly | GO:0060271 | 57 / 237 | 7.9× | 4.69e-35 | 3.64e-31 ✓ sig. |
| cell projection organization | GO:0030030 | 45 / 214 | 6.9× | 3.29e-25 | 1.07e-21 ✓ sig. |
| detection of light stimulus involved in visual perception | GO:0050908 | 17 / 24 | 23.3× | 3.52e-21 | 6.86e-18 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 23 / 57 | 13.3× | 1.60e-20 | 2.73e-17 ✓ sig. |
| photoreceptor cell outer segment organization | GO:0035845 | 13 / 15 | 28.6× | 1.60e-18 | 2.03e-15 ✓ sig. |
| sensory perception of light stimulus | GO:0050953 | 12 / 13 | 30.4× | 6.87e-18 | 8.15e-15 ✓ sig. |
| retina homeostasis | GO:0001895 | 12 / 15 | 26.4× | 2.27e-16 | 2.06e-13 ✓ sig. |
| intraciliary transport | GO:0042073 | 15 / 36 | 13.7× | 4.38e-14 | 2.68e-11 ✓ sig. |
| eye photoreceptor cell development | GO:0042462 | 12 / 21 | 18.8× | 1.24e-13 | 7.02e-11 ✓ sig. |
| retina layer formation | GO:0010842 | 12 / 27 | 14.6× | 6.23e-12 | 2.48e-9 ✓ sig. |
| phototransduction | GO:0007602 | 13 / 34 | 12.6× | 8.34e-12 | 3.24e-9 ✓ sig. |
| kidney development | GO:0001822 | 24 / 146 | 5.4× | 1.39e-11 | 5.16e-9 ✓ sig. |