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.

← Back to all clusters

Cluster 105

12 diseases · 29 shared-gene connections
12 Diseases
11 Unique genes
0.311 Avg. similarity score
Deafness with congenital onychodystrophy Most-connected disease (8 links)
Log in to save this analysis

Save This Analysis

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 with congenital onychodystrophy 8 8 2
Doors syndrome 8 8 2
Periodic paralysis 7 7 2
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 6 6 1
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 6 6 1
Digitrenocerebral syndrome 5 5 3
Infantile myoclonic epilepsy 5 5 2
Deafness-onychodystrophy syndrome 4 4 1
Mitochondrial myopathy with sideroblastic anemia 3 3 4
Zimmermann-laband syndrome 3 3 3
Ataxia with polyneuropathy 2 2 1
Encephalopathy due to mitochondrial and peroxisomal fission defect 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBC1D24 7 / 12 Deafness with congenital onychodystrophy, Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome, Digitrenocerebral syndrome, Doors syndrome and 3 more
ATP6V1B2 5 / 12 Deafness with congenital onychodystrophy, Deafness-onychodystrophy syndrome, Digitrenocerebral syndrome, Doors syndrome and 1 more
ATP6 3 / 12 Ataxia with polyneuropathy, Mitochondrial myopathy with sideroblastic anemia, Periodic paralysis
DNM1L 2 / 12 Encephalopathy due to mitochondrial and peroxisomal fission defect, Mitochondrial myopathy with sideroblastic anemia
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 ⇵
Synaptic vesicle cycle
ATP6V1B2, ATP6V1C1, CPLX1
 KEGG 3 / 79 41.5× 4.35e-5 1.14e-3 ✓ sig.
Ion channel transport
ATP6V1B2, ATP6V1C1
 Reactome 2 / 24 91.0× 2.08e-4 4.03e-3 ✓ sig.
Oxidative phosphorylation
ATP6, ATP6V1B2, ATP6V1C1
 KEGG 3 / 137 23.9× 2.24e-4 4.28e-3 ✓ sig.
Insulin receptor recycling
ATP6V1B2, ATP6V1C1
 Reactome 2 / 26 84.0× 2.45e-4 4.58e-3 ✓ sig.
Collecting duct acid secretion
ATP6V1B2, ATP6V1C1
 KEGG 2 / 28 78.0× 2.85e-4 5.15e-3 ✓ sig.
Transferrin endocytosis and recycling
ATP6V1B2, ATP6V1C1
 Reactome 2 / 31 70.4× 3.50e-4 6.05e-3 ✓ sig.
ROS and RNS production in phagocytes
ATP6V1B2, ATP6V1C1
 Reactome 2 / 34 64.2× 4.21e-4 6.96e-3 ✓ sig.
Vibrio cholerae infection
ATP6V1B2, ATP6V1C1
 KEGG 2 / 51 42.8× 9.49e-4 1.30e-2 ✓ sig.
Amino acids regulate mTORC1
ATP6V1B2, ATP6V1C1
 Reactome 2 / 55 39.7× 1.10e-3 1.46e-2 ✓ sig.
Epithelial cell signaling in Helicobacter pylori infection
ATP6V1B2, ATP6V1C1
 KEGG 2 / 71 30.8× 1.83e-3 2.14e-2 ✓ sig.
Rheumatoid arthritis
ATP6V1B2, ATP6V1C1
 KEGG 2 / 95 23.0× 3.25e-3 3.26e-2 ✓ sig.
Apoptotic execution phase
DNM1L
 Reactome 1 / 4 273× 3.66e-3 3.54e-2 ✓ sig.
tRNA modification in the mitochondrion
PUS1
 Reactome 1 / 6 182× 5.48e-3 4.65e-2 ✓ sig.
Ca2+ activated K+ channels
KCNN3
 Reactome 1 / 9 121× 8.22e-3 6.07e-2
Phagosome
ATP6V1B2, ATP6V1C1
 KEGG 2 / 155 14.1× 8.43e-3 6.18e-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 ⇵
peroxisome fission
DNM1L, MFF
 GO:0016559 2 / 12 283× 2.07e-5 9.23e-4 ✓ sig.
monoatomic ion transport
ATP6, ATP6V1B2, ATP6V1C1, KCNH1, KCNN3
 GO:0006811 5 / 667 12.7× 2.20e-5 9.69e-4 ✓ sig.
mitochondrial fission
DNM1L, MFF
 GO:0000266 2 / 16 212× 3.76e-5 1.45e-3 ✓ sig.
synaptic vesicle lumen acidification
ATP6V1B2, ATP6V1C1
 GO:0097401 2 / 18 189× 4.80e-5 1.74e-3 ✓ sig.
positive regulation of mitochondrial fission
DNM1L, MFF
 GO:0090141 2 / 22 154× 7.23e-5 2.38e-3 ✓ sig.
proton transmembrane transport
ATP6, ATP6V1B2, ATP6V1C1
 GO:1902600 3 / 181 28.2× 1.39e-4 3.86e-3 ✓ sig.
regulation of macroautophagy
ATP6V1B2, ATP6V1C1
 GO:0016241 2 / 57 59.6× 4.94e-4 9.48e-3 ✓ sig.
regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane
CPLX1
 GO:0099145 1 / 1 1,699× 5.89e-4 1.07e-2 ✓ sig.
positive regulation of secretion by cell
DNM1L
 GO:1903532 1 / 1 1,699× 5.89e-4 1.07e-2 ✓ sig.
mitochondrial tyrosyl-tRNA aminoacylation
YARS2
 GO:0070184 1 / 1 1,699× 5.89e-4 1.07e-2 ✓ sig.
mitochondrial tRNA pseudouridine synthesis
PUS1
 GO:0070902 1 / 2 849× 1.18e-3 1.66e-2 ✓ sig.
tyrosyl-tRNA aminoacylation
YARS2
 GO:0006437 1 / 2 849× 1.18e-3 1.66e-2 ✓ sig.
mitochondrial membrane fission
DNM1L
 GO:0090149 1 / 2 849× 1.18e-3 1.66e-2 ✓ sig.
regulation of ATP metabolic process
DNM1L
 GO:1903578 1 / 2 849× 1.18e-3 1.66e-2 ✓ sig.
regulation of peroxisome organization
DNM1L
 GO:1900063 1 / 3 566× 1.76e-3 2.11e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness with congenital onychodystrophy Doors syndrome 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Deafness with congenital onychodystrophy Digitrenocerebral syndrome 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Digitrenocerebral syndrome Doors syndrome 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ataxia with polyneuropathy Periodic paralysis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation Periodic paralysis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Focal epilepsy-intellectual disability-cerebro-cerebellar malformation Infantile myoclonic epilepsy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Doors syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Periodic paralysis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Infantile myoclonic epilepsy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Doors syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness-onychodystrophy syndrome Doors syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness-onychodystrophy syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness with congenital onychodystrophy Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness with congenital onychodystrophy Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness-onychodystrophy syndrome Zimmermann-laband syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Deafness-onychodystrophy syndrome Digitrenocerebral syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Deafness, onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome Digitrenocerebral syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Digitrenocerebral syndrome Focal epilepsy-intellectual disability-cerebro-cerebellar malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Doors syndrome Periodic paralysis 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Deafness with congenital onychodystrophy Infantile myoclonic epilepsy 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Doors syndrome Infantile myoclonic epilepsy 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Infantile myoclonic epilepsy Periodic paralysis 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Deafness with congenital onychodystrophy Periodic paralysis 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Ataxia with polyneuropathy Mitochondrial myopathy with sideroblastic anemia 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Deafness with congenital onychodystrophy Zimmermann-laband syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Doors syndrome Zimmermann-laband syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Mitochondrial myopathy with sideroblastic anemia Periodic paralysis 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Encephalopathy due to mitochondrial and peroxisomal fission defect Mitochondrial myopathy with sideroblastic anemia 0.167 1 5.19e-4 1.04e-3 ✓ sig.