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 286

8 diseases · 13 shared-gene connections
8 Diseases
11 Unique genes
0.252 Avg. similarity score
Deafness, aminoglycoside-induced Most-connected disease (5 links)
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Disease Searched: External ophthalmoplegia 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 ⇵
Deafness, aminoglycoside-induced 5 5 4
Deafness, sensorineural, autosomal-mitochondrial type 5 5 2
Chorioretinal atrophy 4 4 3
Recurrent myoglobinuria mitochondrial 4 4 2
Deafness, nonsyndromic sensorineural, mitochondrial 3 3 5
External ophthalmoplegia 3 3 1
Mitochondrial encephalopathy 1 1 3
Retinitis pigmentosa-12, autosomal recessive 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COX1 5 / 8 Chorioretinal atrophy, Deafness, aminoglycoside-induced, Deafness, nonsyndromic sensorineural, mitochondrial, Deafness, sensorineural, autosomal-mitochondrial type and 1 more
ND1 4 / 8 Deafness, aminoglycoside-induced, Deafness, nonsyndromic sensorineural, mitochondrial, Deafness, sensorineural, autosomal-mitochondrial type, External ophthalmoplegia
COX3 2 / 8 Mitochondrial encephalopathy, Recurrent myoglobinuria mitochondrial
CRB1 2 / 8 Chorioretinal atrophy, Retinitis pigmentosa-12, autosomal recessive
RNR1 2 / 8 Deafness, aminoglycoside-induced, Deafness, nonsyndromic sensorineural, mitochondrial
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 ⇵
Respiratory electron transport
COX1, ND1, COX3
 Reactome 3 / 83 39.5× 5.05e-5 1.10e-3 ✓ sig.
Oxidative phosphorylation
COX1, ND1, COX3
 KEGG 3 / 137 23.9× 2.24e-4 3.59e-3 ✓ sig.
Diabetic cardiomyopathy
COX1, ND1, COX3
 KEGG 3 / 205 16.0× 7.31e-4 8.94e-3 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
COX1, ND1, COX3
 KEGG 3 / 227 14.4× 9.83e-4 1.12e-2 ✓ sig.
Thermogenesis
COX1, ND1, COX3
 KEGG 3 / 234 14.0× 1.07e-3 1.20e-2 ✓ sig.
Parkinson disease
COX1, ND1, COX3
 KEGG 3 / 268 12.2× 1.59e-3 1.61e-2 ✓ sig.
Prion disease
COX1, ND1, COX3
 KEGG 3 / 275 11.9× 1.71e-3 1.70e-2 ✓ sig.
Huntington disease
COX1, ND1, COX3
 KEGG 3 / 308 10.6× 2.37e-3 2.15e-2 ✓ sig.
TP53 Regulates Metabolic Genes
COX1, COX3
 Reactome 2 / 86 25.4× 2.67e-3 2.35e-2 ✓ sig.
Cardiac muscle contraction
COX1, COX3
 KEGG 2 / 87 25.1× 2.73e-3 2.39e-2 ✓ sig.
Amyotrophic lateral sclerosis
COX1, ND1, COX3
 KEGG 3 / 368 8.9× 3.92e-3 3.09e-2 ✓ sig.
Alzheimer disease
COX1, ND1, COX3
 KEGG 3 / 388 8.4× 4.55e-3 3.43e-2 ✓ sig.
Pathways of neurodegeneration - multiple diseases
COX1, ND1, COX3
 KEGG 3 / 480 6.8× 8.23e-3 5.04e-2
Non-alcoholic fatty liver disease
COX1, COX3
 KEGG 2 / 157 13.9× 8.64e-3 5.20e-2
TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain
CHM
 Reactome 1 / 14 78.0× 1.28e-2 6.57e-2

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 electron transport, cytochrome c to oxygen
COX1, COX3
 GO:0006123 2 / 23 148× 7.92e-5 2.60e-3 ✓ sig.
respiratory electron transport chain
COX1, COX3
 GO:0022904 2 / 23 148× 7.92e-5 2.60e-3 ✓ sig.
proton transmembrane transport
COX1, ND1, COX3
 GO:1902600 3 / 181 28.2× 1.39e-4 3.92e-3 ✓ sig.
mitochondrial respiratory chain complex I assembly
ND1, FOXRED1
 GO:0032981 2 / 40 84.9× 2.43e-4 5.82e-3 ✓ sig.
cellular respiration
COX1, COX3
 GO:0045333 2 / 41 82.9× 2.55e-4 6.04e-3 ✓ sig.
aerobic respiration
COX1, ND1
 GO:0009060 2 / 68 50.0× 7.03e-4 1.19e-2 ✓ sig.
post-embryonic retina morphogenesis in camera-type eye
CRB1
 GO:0060060 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
establishment of bipolar cell polarity involved in cell morphogenesis
CRB1
 GO:0061159 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
aerobic electron transport chain
COX3
 GO:0019646 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
tRNA wobble position uridine thiolation
TRMU
 GO:0002143 1 / 4 425× 2.35e-3 2.30e-2 ✓ sig.
negative regulation of mesenchymal cell apoptotic process
POU3F4
 GO:2001054 1 / 6 283× 3.53e-3 2.82e-2 ✓ sig.
protein geranylgeranylation
CHM
 GO:0018344 1 / 6 283× 3.53e-3 2.82e-2 ✓ sig.
mitochondrial membrane organization
TIMM50
 GO:0007006 1 / 7 243× 4.11e-3 3.04e-2 ✓ sig.
response to hypoxia
COX1, ND1
 GO:0001666 2 / 176 19.3× 4.59e-3 3.22e-2 ✓ sig.
response to hydroperoxide
ND1
 GO:0033194 1 / 9 189× 5.29e-3 3.43e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness, aminoglycoside-induced Deafness, nonsyndromic sensorineural, mitochondrial 0.429 3 6.46e-11 6.13e-10 ✓ sig.
Deafness, aminoglycoside-induced Deafness, sensorineural, autosomal-mitochondrial type 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Deafness, nonsyndromic sensorineural, mitochondrial Deafness, sensorineural, autosomal-mitochondrial type 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Deafness, sensorineural, autosomal-mitochondrial type External ophthalmoplegia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chorioretinal atrophy Retinitis pigmentosa-12, autosomal recessive 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Deafness, sensorineural, autosomal-mitochondrial type Recurrent myoglobinuria mitochondrial 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Deafness, aminoglycoside-induced External ophthalmoplegia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Deafness, nonsyndromic sensorineural, mitochondrial External ophthalmoplegia 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Chorioretinal atrophy Deafness, sensorineural, autosomal-mitochondrial type 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Chorioretinal atrophy Recurrent myoglobinuria mitochondrial 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Mitochondrial encephalopathy Recurrent myoglobinuria mitochondrial 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Deafness, aminoglycoside-induced Recurrent myoglobinuria mitochondrial 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Chorioretinal atrophy Deafness, aminoglycoside-induced 0.143 1 7.75e-4 1.25e-3 ✓ sig.