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 244

7 diseases · 13 shared-gene connections
7 Diseases
4 Unique genes
0.415 Avg. similarity score
Deafness, nonsyndromic sensorineural, mitochondrial Most-connected disease (6 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 ⇵
Deafness, nonsyndromic sensorineural, mitochondrial 6 6 3
Ayazi syndrome 4 4 1
Choroideremia-deafness-obesity syndrome 4 4 1
Chromosome xq21 deletion syndrome 4 4 1
Xq21 microdeletion syndrome 4 4 1
Deafness, aminoglycoside-induced 2 2 3
Deafness, sensorineural, autosomal-mitochondrial type 2 2 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
POU3F4 5 / 7 Ayazi syndrome, Choroideremia-deafness-obesity syndrome, Chromosome xq21 deletion syndrome, Deafness, nonsyndromic sensorineural, mitochondrial and 1 more
COX1 3 / 7 Deafness, aminoglycoside-induced, Deafness, nonsyndromic sensorineural, mitochondrial, Deafness, sensorineural, autosomal-mitochondrial type
ND1 3 / 7 Deafness, aminoglycoside-induced, Deafness, nonsyndromic sensorineural, mitochondrial, Deafness, sensorineural, autosomal-mitochondrial type
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
 Reactome 2 / 83 72.3× 2.81e-4 5.10e-3 ✓ sig.
Oxidative phosphorylation
COX1, ND1
 KEGG 2 / 137 43.8× 7.64e-4 1.11e-2 ✓ sig.
Diabetic cardiomyopathy
COX1, ND1
 KEGG 2 / 205 29.3× 1.70e-3 2.03e-2 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
COX1, ND1
 KEGG 2 / 227 26.5× 2.08e-3 2.35e-2 ✓ sig.
Thermogenesis
COX1, ND1
 KEGG 2 / 234 25.7× 2.21e-3 2.46e-2 ✓ sig.
Parkinson disease
COX1, ND1
 KEGG 2 / 268 22.4× 2.89e-3 3.00e-2 ✓ sig.
Prion disease
COX1, ND1
 KEGG 2 / 275 21.8× 3.04e-3 3.10e-2 ✓ sig.
Huntington disease
COX1, ND1
 KEGG 2 / 308 19.5× 3.80e-3 3.64e-2 ✓ sig.
Amyotrophic lateral sclerosis
COX1, ND1
 KEGG 2 / 368 16.3× 5.39e-3 4.60e-2 ✓ sig.
Alzheimer disease
COX1, ND1
 KEGG 2 / 388 15.5× 5.98e-3 4.92e-2 ✓ sig.
Pathways of neurodegeneration - multiple diseases
COX1, ND1
 KEGG 2 / 480 12.5× 9.06e-3 6.47e-2
Complex I biogenesis
ND1
 Reactome 1 / 55 54.6× 1.82e-2 9.77e-2
TP53 Regulates Metabolic Genes
COX1
 Reactome 1 / 86 34.9× 2.83e-2 1.25e-1
Cardiac muscle contraction
COX1
 KEGG 1 / 87 34.5× 2.87e-2 1.26e-1
Retrograde endocannabinoid signaling
ND1
 KEGG 1 / 149 20.2× 4.87e-2 1.69e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
aerobic respiration
COX1, ND1
 GO:0009060 2 / 68 137× 7.79e-5 2.52e-3 ✓ sig.
response to hypoxia
COX1, ND1
 GO:0001666 2 / 176 53.1× 5.23e-4 9.86e-3 ✓ sig.
proton transmembrane transport
COX1, ND1
 GO:1902600 2 / 181 51.6× 5.53e-4 1.02e-2 ✓ sig.
tRNA wobble position uridine thiolation
TRMU
 GO:0002143 1 / 4 1,168× 8.56e-4 1.36e-2 ✓ sig.
negative regulation of mesenchymal cell apoptotic process
POU3F4
 GO:2001054 1 / 6 779× 1.28e-3 1.75e-2 ✓ sig.
response to hydroperoxide
ND1
 GO:0033194 1 / 9 519× 1.93e-3 2.20e-2 ✓ sig.
response to copper ion
COX1
 GO:0046688 1 / 12 389× 2.57e-3 2.58e-2 ✓ sig.
mitochondrial electron transport, cytochrome c to oxygen
COX1
 GO:0006123 1 / 23 203× 4.91e-3 3.63e-2 ✓ sig.
respiratory electron transport chain
COX1
 GO:0022904 1 / 23 203× 4.91e-3 3.63e-2 ✓ sig.
response to electrical stimulus
COX1
 GO:0051602 1 / 24 195× 5.13e-3 3.71e-2 ✓ sig.
oxidative phosphorylation
COX1
 GO:0006119 1 / 27 173× 5.77e-3 3.94e-2 ✓ sig.
cochlea morphogenesis
POU3F4
 GO:0090103 1 / 28 167× 5.98e-3 4.01e-2 ✓ sig.
mitochondrial respiratory chain complex I assembly
ND1
 GO:0032981 1 / 40 117× 8.54e-3 4.72e-2 ✓ sig.
cellular respiration
COX1
 GO:0045333 1 / 41 114× 8.75e-3 4.79e-2 ✓ sig.
mitochondrial electron transport, NADH to ubiquinone
ND1
 GO:0006120 1 / 47 99.4× 1.00e-2 5.14e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness, aminoglycoside-induced Deafness, sensorineural, autosomal-mitochondrial type 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Deafness, nonsyndromic sensorineural, mitochondrial Deafness, sensorineural, autosomal-mitochondrial type 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Deafness, aminoglycoside-induced Deafness, nonsyndromic sensorineural, mitochondrial 0.400 2 7.59e-8 5.72e-7 ✓ sig.
Ayazi syndrome Choroideremia-deafness-obesity syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ayazi syndrome Chromosome xq21 deletion syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ayazi syndrome Xq21 microdeletion syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Choroideremia-deafness-obesity syndrome Chromosome xq21 deletion syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Choroideremia-deafness-obesity syndrome Xq21 microdeletion syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome xq21 deletion syndrome Xq21 microdeletion syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ayazi syndrome Deafness, nonsyndromic sensorineural, mitochondrial 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Choroideremia-deafness-obesity syndrome Deafness, nonsyndromic sensorineural, mitochondrial 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Chromosome xq21 deletion syndrome Deafness, nonsyndromic sensorineural, mitochondrial 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Deafness, nonsyndromic sensorineural, mitochondrial Xq21 microdeletion syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.