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 26

19 diseases · 47 shared-gene connections
19 Diseases
139 Unique genes
0.195 Avg. similarity score
Melas syndrome Most-connected disease (12 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Melas syndrome 12 12 18
Neuropathy, ataxia, and retinitis pigmentosa 10 10 13
Cleft palate and bilateral cleft lip 9 9 14
Developmental delay 8 8 38
Postaxial polydactyly 8 8 21
Optic neuropathy 7 7 9
Leber hereditary optic neuropathy 6 6 28
Congenital cardiomyopathy 5 5 2
Periodic paralysis with later-onset distal motor neuropathy 5 5 1
Rod-cone dystrophy 5 5 33
Bicuspid aortic valve 4 4 14
Myoclonic epilepsy with ragged red fibers 4 4 3
Mitochondrial myopathy 3 3 15
Progressive external ophthalmoplegia 3 3 13
Developmental delay with hypotonia and impaired language 1 1 1
Developmental delay with variable neurological abnormalities 1 1 1
Intellectual developmental disorder seizures language 1 1 1
Stomatitis 1 1 11
aortic valve disease 3 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
ATP8 9 / 19 Bicuspid aortic valve, Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome and 5 more
ND4 9 / 19 Cleft palate and bilateral cleft lip, Congenital cardiomyopathy, Developmental delay, Leber hereditary optic neuropathy and 5 more
ND5 9 / 19 Cleft palate and bilateral cleft lip, Congenital cardiomyopathy, Developmental delay, Leber hereditary optic neuropathy and 5 more
ATP6 8 / 19 Bicuspid aortic valve, Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome and 4 more
COX3 7 / 19 Cleft palate and bilateral cleft lip, Developmental delay, Leber hereditary optic neuropathy, Melas syndrome and 3 more
ND1 7 / 19 Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome, Neuropathy, ataxia, and retinitis pigmentosa and 3 more
ND2 7 / 19 Cleft palate and bilateral cleft lip, Developmental delay, Leber hereditary optic neuropathy, Melas syndrome and 3 more
COX1 6 / 19 Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome, Neuropathy, ataxia, and retinitis pigmentosa and 2 more
COX2 6 / 19 Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome, Neuropathy, ataxia, and retinitis pigmentosa and 2 more
ND3 6 / 19 Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Melas syndrome, Neuropathy, ataxia, and retinitis pigmentosa and 2 more
IL1A 5 / 19 Leber hereditary optic neuropathy, Melas syndrome, Mitochondrial myopathy, Myoclonic epilepsy with ragged red fibers and 1 more
IL1B 5 / 19 Leber hereditary optic neuropathy, Melas syndrome, Mitochondrial myopathy, Myoclonic epilepsy with ragged red fibers and 1 more
ND4L 5 / 19 Cleft palate and bilateral cleft lip, Leber hereditary optic neuropathy, Neuropathy, ataxia, and retinitis pigmentosa, Postaxial polydactyly and 1 more
CYTB 4 / 19 Developmental delay, Leber hereditary optic neuropathy, Melas syndrome, Mitochondrial myopathy
RRM2B 3 / 19 Mitochondrial myopathy, Progressive external ophthalmoplegia, Rod-cone dystrophy
SOD2 3 / 19 Leber hereditary optic neuropathy, Melas syndrome, Progressive external ophthalmoplegia
BBIP1 2 / 19 Postaxial polydactyly, Rod-cone dystrophy
CSF3 2 / 19 Optic neuropathy, Stomatitis
FBXW7 2 / 19 Developmental delay, Developmental delay with hypotonia and impaired language
IFNA2 2 / 19 Optic neuropathy, Stomatitis
LMBRD2 2 / 19 Developmental delay, Developmental delay with variable neurological abnormalities
LRAT 2 / 19 Leber hereditary optic neuropathy, Rod-cone dystrophy
ND6 2 / 19 Leber hereditary optic neuropathy, Melas syndrome
PIGL 2 / 19 Cleft palate and bilateral cleft lip, Postaxial polydactyly
POLG 2 / 19 Melas syndrome, Progressive external ophthalmoplegia
ROBO4 2 / 19 aortic valve disease 3, Bicuspid aortic valve
RPE65 2 / 19 Leber hereditary optic neuropathy, Rod-cone dystrophy
SETD1B 2 / 19 Developmental delay, Intellectual developmental disorder seizures language
SLC25A4 2 / 19 Mitochondrial myopathy, Progressive external ophthalmoplegia
SOD1 2 / 19 Melas syndrome, Progressive external ophthalmoplegia
TK2 2 / 19 Mitochondrial myopathy, Progressive external ophthalmoplegia
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 ⇵
Prion disease
SLC25A4, ATP6, ATP8, NOTCH1, IL1A, IL1B, SOD1, COX1, COX2, COX3, ND1, ND2
 KEGG 24 / 275 7.5× 8.00e-15 2.56e-12 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
SLC25A4, ATP6, ATP8, SOD1, SOD2, COX1, COX2, COX3, ND1, ND2, ND3, ND4
 KEGG 20 / 227 7.6× 1.43e-12 3.05e-10 ✓ sig.
Diabetic cardiomyopathy
SLC25A4, ATP6, ATP8, COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 18 / 205 7.6× 2.17e-11 3.60e-9 ✓ sig.
Oxidative phosphorylation
ATP6, ATP8, COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND4L, ND5, CYTB
 KEGG 15 / 137 9.5× 4.87e-11 7.51e-9 ✓ sig.
Huntington disease
SLC25A4, ATP6, ATP8, SOD1, SOD2, COX1, COX2, COX3, ND1, ND2, ND3, ND4
 KEGG 21 / 308 5.9× 5.14e-11 7.89e-9 ✓ sig.
Respiratory electron transport
COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND5, CYTB, NDUFS2, ND6, NDUFS1
 Reactome 12 / 83 12.5× 1.72e-10 2.37e-8 ✓ sig.
Parkinson disease
SLC25A4, ATP6, ATP8, SOD1, COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND4L
 KEGG 19 / 268 6.1× 2.39e-10 3.16e-8 ✓ sig.
Alzheimer disease
SLC25A4, ATP6, ATP8, IL1A, IL1B, COX1, COX2, COX3, ND1, ND2, ND3, ND4
 KEGG 22 / 388 4.9× 5.96e-10 7.05e-8 ✓ sig.
Amyotrophic lateral sclerosis
ATP6, ATP8, SOD1, COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND4L, ND5
 KEGG 21 / 368 4.9× 1.36e-9 1.46e-7 ✓ sig.
Pathways of neurodegeneration - multiple diseases
SLC25A4, ATP6, ATP8, IL1A, IL1B, SOD1, COX1, COX2, COX3, ND1, ND2, ND3
 KEGG 23 / 480 4.1× 6.02e-9 5.64e-7 ✓ sig.
Complex I biogenesis
ND1, ND2, ND3, ND4, ND5, NDUFS2, ND6, NDUFAF5, NDUFS1
 Reactome 9 / 55 14.1× 1.16e-8 9.92e-7 ✓ sig.
Thermogenesis
ATP6, ATP8, COX1, COX2, COX3, ND1, ND2, ND3, ND4, ND4L, ND5, CYTB
 KEGG 16 / 234 5.9× 1.17e-8 9.94e-7 ✓ sig.
Retrograde endocannabinoid signaling
ND1, ND2, ND3, ND4, ND4L, ND5, GNAO1, NDUFS2, ND6, NDUFS1
 KEGG 10 / 149 5.8× 8.67e-6 2.98e-4 ✓ sig.
Non-alcoholic fatty liver disease
IL1A, IL1B, COX1, COX2, COX3, CYTB, NDUFS2, NDUFS1, IL6, TNF
 KEGG 10 / 157 5.5× 1.37e-5 4.37e-4 ✓ sig.
The canonical retinoid cycle in rods (twilight vision)
LRAT, RDH12, RPE65, RHO
 Reactome 4 / 20 17.3× 7.21e-5 1.71e-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 ⇵
mitochondrial DNA replication
POLG, POLG2, POLRMT, RRM2B, TWNK, RRM1, DNA2
 GO:0006264 7 / 11 85.6× 3.48e-13 1.74e-10 ✓ sig.
proton motive force-driven mitochondrial ATP synthesis
ATP6, ATP8, ND1, ND2, ND3, ND4, ND4L, ND5, NDUFS2, ND6, NDUFS1
 GO:0042776 11 / 64 23.1× 1.37e-12 6.13e-10 ✓ sig.
proton transmembrane transport
SLC25A4, ATP6, ATP8, SLC2A10, COX1, COX2, COX3, ND1, ND2, ND3, ND4L, SLC25A22
 GO:1902600 15 / 181 11.1× 5.93e-12 2.29e-9 ✓ sig.
mitochondrial respiratory chain complex I assembly
ND1, ND2, ND4, ND5, FOXRED1, NDUFS2, ND6, NDUFAF5, NDUFS1
 GO:0032981 9 / 40 30.2× 1.21e-11 4.38e-9 ✓ sig.
mitochondrial electron transport, NADH to ubiquinone
ND1, ND2, ND3, ND4, ND4L, ND5, NDUFS2, ND6, NDUFS1
 GO:0006120 9 / 47 25.7× 5.75e-11 1.75e-8 ✓ sig.
aerobic respiration
COX1, ND1, ND2, ND3, ND4, ND4L, ND5, NDUFS2, ND6, NDUFS1
 GO:0009060 10 / 68 19.8× 7.53e-11 2.21e-8 ✓ sig.
ATP synthesis coupled electron transport
COX2, ND4, ND4L, ND5, NDUFS1
 GO:0042773 5 / 7 96.0× 4.40e-10 1.07e-7 ✓ sig.
cilium assembly
NOTCH1, FLNA, USP9X, CIBAR1, AHI1, BBIP1, CEP290, CFAP20, IFT122, IFT88, INPP5E, KIAA0586
 GO:0060271 12 / 237 6.8× 2.11e-7 2.27e-5 ✓ sig.
visual perception
LRAT, RDH12, RP1, RPE65, RPGRIP1, BEST1, EYS, PDE6B, RHO, USH2A, BBS10
 GO:0007601 11 / 215 6.9× 6.24e-7 5.64e-5 ✓ sig.
response to copper ion
IL1A, SOD1, COX1, CYTB
 GO:0046688 4 / 12 44.8× 1.39e-6 1.07e-4 ✓ sig.
electron transport coupled proton transport
ND4, ND5, CYTB
 GO:0015990 3 / 4 101× 1.60e-6 1.21e-4 ✓ sig.
response to ethanol
SOD1, COX2, ND4, CYTB, GRIN2B, TNF, CSF3, NTRK3
 GO:0045471 8 / 110 9.8× 1.66e-6 1.24e-4 ✓ sig.
retina development in camera-type eye
RRM1, RP1, RPGRIP1, PDE6B, RHO, SCAPER, BBS10
 GO:0060041 7 / 85 11.1× 3.30e-6 2.15e-4 ✓ sig.
cell projection organization
FLNA, PRICKLE3, RP1, CIBAR1, AHI1, BBIP1, CEP290, IFT122, IFT88, KIAA0586
 GO:0030030 10 / 214 6.3× 4.63e-6 2.83e-4 ✓ sig.
response to hypoxia
SOD2, COX1, COX2, ND1, ND2, ND4, ND5, CYTB, TNF
 GO:0001666 9 / 176 6.9× 6.82e-6 3.84e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Leber hereditary optic neuropathy Melas syndrome 0.469 15 6.19e-41 2.80e-39 ✓ sig.
Cleft palate and bilateral cleft lip Postaxial polydactyly 0.500 12 7.24e-35 2.74e-33 ✓ sig.
Cleft palate and bilateral cleft lip Neuropathy, ataxia, and retinitis pigmentosa 0.647 11 9.85e-35 3.72e-33 ✓ sig.
Neuropathy, ataxia, and retinitis pigmentosa Postaxial polydactyly 0.458 11 9.54e-32 3.24e-30 ✓ sig.
Leber hereditary optic neuropathy Neuropathy, ataxia, and retinitis pigmentosa 0.355 11 5.80e-30 1.87e-28 ✓ sig.
Cleft palate and bilateral cleft lip Leber hereditary optic neuropathy 0.344 11 2.71e-29 8.49e-28 ✓ sig.
Leber hereditary optic neuropathy Rod-cone dystrophy 0.265 13 4.82e-29 1.51e-27 ✓ sig.
Neuropathy, ataxia, and retinitis pigmentosa Rod-cone dystrophy 0.306 11 5.23e-29 1.63e-27 ✓ sig.
Melas syndrome Neuropathy, ataxia, and retinitis pigmentosa 0.455 10 6.07e-29 1.89e-27 ✓ sig.
Cleft palate and bilateral cleft lip Melas syndrome 0.435 10 2.12e-28 6.47e-27 ✓ sig.
Cleft palate and bilateral cleft lip Rod-cone dystrophy 0.297 11 2.44e-28 7.41e-27 ✓ sig.
Postaxial polydactyly Rod-cone dystrophy 0.279 12 2.79e-28 8.46e-27 ✓ sig.
Leber hereditary optic neuropathy Postaxial polydactyly 0.282 11 2.60e-26 7.16e-25 ✓ sig.
Melas syndrome Postaxial polydactyly 0.333 10 7.46e-26 2.00e-24 ✓ sig.
Melas syndrome Rod-cone dystrophy 0.238 10 1.95e-23 4.61e-22 ✓ sig.
Mitochondrial myopathy Progressive external ophthalmoplegia 0.208 5 5.34e-13 6.99e-12 ✓ sig.
Melas syndrome Progressive external ophthalmoplegia 0.185 5 1.52e-12 1.92e-11 ✓ sig.
Neuropathy, ataxia, and retinitis pigmentosa Optic neuropathy 0.211 4 3.84e-11 4.20e-10 ✓ sig.
Cleft palate and bilateral cleft lip Optic neuropathy 0.200 4 5.37e-11 5.83e-10 ✓ sig.
Melas syndrome Optic neuropathy 0.167 4 1.64e-10 1.69e-9 ✓ sig.
Optic neuropathy Postaxial polydactyly 0.148 4 3.21e-10 3.23e-9 ✓ sig.
Developmental delay Melas syndrome 0.096 5 5.83e-10 5.70e-9 ✓ sig.
Melas syndrome Myoclonic epilepsy with ragged red fibers 0.158 3 1.34e-9 1.27e-8 ✓ sig.
Developmental delay Leber hereditary optic neuropathy 0.081 5 6.57e-9 5.81e-8 ✓ sig.
Developmental delay Neuropathy, ataxia, and retinitis pigmentosa 0.083 4 2.22e-8 1.82e-7 ✓ sig.
Cleft palate and bilateral cleft lip Developmental delay 0.082 4 3.10e-8 2.48e-7 ✓ sig.
Developmental delay Postaxial polydactyly 0.071 4 1.83e-7 1.29e-6 ✓ sig.
Melas syndrome Mitochondrial myopathy 0.097 3 6.05e-7 3.90e-6 ✓ sig.
Congenital cardiomyopathy Neuropathy, ataxia, and retinitis pigmentosa 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Cleft palate and bilateral cleft lip Congenital cardiomyopathy 0.133 2 7.68e-7 4.83e-6 ✓ sig.
Congenital cardiomyopathy Melas syndrome 0.105 2 1.29e-6 7.84e-6 ✓ sig.
Congenital cardiomyopathy Postaxial polydactyly 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Myoclonic epilepsy with ragged red fibers Progressive external ophthalmoplegia 0.133 2 1.97e-6 1.16e-5 ✓ sig.
Mitochondrial myopathy Myoclonic epilepsy with ragged red fibers 0.118 2 2.66e-6 1.53e-5 ✓ sig.
Optic neuropathy Stomatitis 0.105 2 1.67e-5 8.44e-5 ✓ sig.
Bicuspid aortic valve Optic neuropathy 0.091 2 2.75e-5 1.35e-4 ✓ sig.
Bicuspid aortic valve Neuropathy, ataxia, and retinitis pigmentosa 0.077 2 5.95e-5 2.34e-4 ✓ sig.
Congenital cardiomyopathy Myoclonic epilepsy with ragged red fibers 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Optic neuropathy Periodic paralysis with later-onset distal motor neuropathy 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Neuropathy, ataxia, and retinitis pigmentosa Periodic paralysis with later-onset distal motor neuropathy 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Bicuspid aortic valve Periodic paralysis with later-onset distal motor neuropathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Cleft palate and bilateral cleft lip Periodic paralysis with later-onset distal motor neuropathy 0.067 1 9.09e-4 1.56e-3 ✓ sig.
aortic valve disease 3 Bicuspid aortic valve 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Melas syndrome Periodic paralysis with later-onset distal motor neuropathy 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Developmental delay Intellectual developmental disorder seizures language 0.026 1 2.47e-3 3.36e-3 ✓ sig.
Developmental delay Developmental delay with variable neurological abnormalities 0.026 1 2.47e-3 3.36e-3 ✓ sig.
Developmental delay Developmental delay with hypotonia and impaired language 0.026 1 2.47e-3 3.36e-3 ✓ sig.