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 94

12 diseases · 31 shared-gene connections
12 Diseases
27 Unique genes
0.238 Avg. similarity score
Rothmund-thomson syndrome Most-connected disease (10 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 ⇵
Rothmund-thomson syndrome 10 10 12
Benign pemphigus 9 9 9
Accessory skin tag 8 8 8
Darier disease 8 8 9
Cutis laxa 6 6 20
autosomal recessive cutis laxa type 2B 5 5 1
autosomal recessive cutis laxa type 2C 5 5 1
Demyelinating hereditary motor and sensory neuropathy 4 4 2
autosomal recessive cutis laxa type 2D 4 4 1
Benign familial pemphigus 1 1 1
Dna2-related mitochondrial dna deletion syndrome 1 1 1
Rothmund-Thomson syndrome type 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ATP6V1A 6 / 12 Accessory skin tag, autosomal recessive cutis laxa type 2D, Benign pemphigus, Cutis laxa and 2 more
ATP6V1E1 6 / 12 Accessory skin tag, autosomal recessive cutis laxa type 2C, Benign pemphigus, Cutis laxa and 2 more
FBLN5 6 / 12 Accessory skin tag, Benign pemphigus, Cutis laxa, Darier disease and 2 more
PYCR1 6 / 12 Accessory skin tag, autosomal recessive cutis laxa type 2B, Benign pemphigus, Cutis laxa and 2 more
ALDH18A1 5 / 12 Accessory skin tag, Benign pemphigus, Cutis laxa, Darier disease and 1 more
ATP6V0A2 5 / 12 Accessory skin tag, Benign pemphigus, Cutis laxa, Darier disease and 1 more
EFEMP2 5 / 12 Accessory skin tag, Benign pemphigus, Cutis laxa, Darier disease and 1 more
ELN 5 / 12 Accessory skin tag, Benign pemphigus, Cutis laxa, Darier disease and 1 more
ANAPC1 2 / 12 Rothmund-thomson syndrome, Rothmund-Thomson syndrome type 1
ATP2C1 2 / 12 Benign familial pemphigus, Benign pemphigus
DNA2 2 / 12 Dna2-related mitochondrial dna deletion syndrome, Rothmund-thomson syndrome
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 ⇵
Molecules associated with elastic fibres
ELN, FBLN5, EFEMP2, LTBP1, EFEMP1, LTBP4
 Reactome 6 / 38 70.2× 1.87e-10 2.54e-8 ✓ sig.
Elastic fibre formation
ELN, FBLN5, LOX
 Reactome 3 / 18 74.1× 8.08e-6 2.81e-4 ✓ sig.
Ion channel transport
ATP6V0A2, ATP6V1A, ATP6V1E1
 Reactome 3 / 24 55.6× 1.99e-5 5.95e-4 ✓ sig.
Insulin receptor recycling
ATP6V0A2, ATP6V1A, ATP6V1E1
 Reactome 3 / 26 51.3× 2.55e-5 7.26e-4 ✓ sig.
Collecting duct acid secretion
ATP6V0A2, ATP6V1A, ATP6V1E1
 KEGG 3 / 28 47.7× 3.20e-5 8.81e-4 ✓ sig.
Transferrin endocytosis and recycling
ATP6V0A2, ATP6V1A, ATP6V1E1
 Reactome 3 / 31 43.0× 4.37e-5 1.14e-3 ✓ sig.
ROS and RNS production in phagocytes
ATP6V0A2, ATP6V1A, ATP6V1E1
 Reactome 3 / 34 39.2× 5.79e-5 1.44e-3 ✓ sig.
Vibrio cholerae infection
ATP6V0A2, ATP6V1A, ATP6V1E1
 KEGG 3 / 51 26.2× 1.96e-4 3.85e-3 ✓ sig.
Ion transport by P-type ATPases
ATP7A, ATP2A2, ATP2C1
 Reactome 3 / 56 23.8× 2.59e-4 4.79e-3 ✓ sig.
Glutamate and glutamine metabolism
ALDH18A1, PYCR1
 Reactome 2 / 14 63.5× 4.36e-4 7.15e-3 ✓ sig.
Epithelial cell signaling in Helicobacter pylori infection
ATP6V0A2, ATP6V1A, ATP6V1E1
 KEGG 3 / 71 18.8× 5.23e-4 8.24e-3 ✓ sig.
Synaptic vesicle cycle
ATP6V0A2, ATP6V1A, ATP6V1E1
 KEGG 3 / 79 16.9× 7.15e-4 1.05e-2 ✓ sig.
Rheumatoid arthritis
ATP6V0A2, ATP6V1A, ATP6V1E1
 KEGG 3 / 95 14.0× 1.22e-3 1.58e-2 ✓ sig.
Defective ABCC6 causes pseudoxanthoma elasticum (PXE)
ABCC6
 Reactome 1 / 1 445× 2.25e-3 2.48e-2 ✓ sig.
Resolution of D-loop Structures through Holliday Junction Intermediates
MUS81, DNA2
 Reactome 2 / 33 27.0× 2.46e-3 2.66e-2 ✓ 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 ⇵
elastic fiber assembly
FBLN5, EFEMP2, ATP7A, LOX, LTBP4
 GO:0048251 5 / 11 315× 1.95e-12 8.42e-10 ✓ sig.
ATP metabolic process
ATP6V1A, ABCC6, ATP7A
 GO:0046034 3 / 36 57.7× 1.86e-5 8.46e-4 ✓ sig.
L-proline biosynthetic process
ALDH18A1, PYCR1
 GO:0055129 2 / 6 231× 3.00e-5 1.22e-3 ✓ sig.
monoatomic ion transport
ATP6V0A2, ATP6V1A, ATP6V1E1, ATP7A, SLC39A13, ATP2A2, ATP2C1
 GO:0006811 7 / 667 7.3× 3.40e-5 1.35e-3 ✓ sig.
connective tissue development
LOX, SLC39A13
 GO:0061448 2 / 7 198× 4.20e-5 1.58e-3 ✓ sig.
cellular response to increased oxygen levels
ATP6V0A2, ATP6V1A
 GO:0036295 2 / 8 173× 5.60e-5 1.96e-3 ✓ sig.
regulation of macroautophagy
ATP6V0A2, ATP6V1A, ATP6V1E1
 GO:0016241 3 / 57 36.4× 7.47e-5 2.44e-3 ✓ sig.
Golgi lumen acidification
ATP6V0A2, ATP6V1A
 GO:0061795 2 / 10 138× 8.98e-5 2.79e-3 ✓ sig.
collagen fibril organization
ATP7A, COL5A1, LOX
 GO:0030199 3 / 65 31.9× 1.11e-4 3.26e-3 ✓ sig.
telomere maintenance
MUS81, DNA2, RECQL4
 GO:0000723 3 / 66 31.5× 1.16e-4 3.38e-3 ✓ sig.
blood vessel development
ATP7A, COL5A1, LOX
 GO:0001568 3 / 70 29.7× 1.38e-4 3.84e-3 ✓ sig.
synaptic vesicle lumen acidification
ATP6V1A, ATP6V1E1
 GO:0097401 2 / 18 76.9× 3.03e-4 6.77e-3 ✓ sig.
vacuolar acidification
ATP6V0A2, ATP6V1A
 GO:0007035 2 / 23 60.2× 4.99e-4 9.56e-3 ✓ sig.
regulation of transforming growth factor beta receptor signaling pathway
LOX, LTBP4
 GO:0017015 2 / 24 57.7× 5.44e-4 1.01e-2 ✓ sig.
amino acid biosynthetic process
ALDH18A1, PYCR1
 GO:0008652 2 / 27 51.3× 6.90e-4 1.19e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Accessory skin tag Darier disease 0.800 8 1.15e-28 3.53e-27 ✓ sig.
Accessory skin tag Benign pemphigus 0.800 8 1.15e-28 3.53e-27 ✓ sig.
Benign pemphigus Darier disease 0.727 8 1.04e-27 3.07e-26 ✓ sig.
Accessory skin tag Rothmund-thomson syndrome 0.615 8 6.33e-27 1.81e-25 ✓ sig.
Darier disease Rothmund-thomson syndrome 0.571 8 5.69e-26 1.54e-24 ✓ sig.
Benign pemphigus Rothmund-thomson syndrome 0.571 8 5.69e-26 1.54e-24 ✓ sig.
Accessory skin tag Cutis laxa 0.381 8 1.61e-24 4.03e-23 ✓ sig.
Cutis laxa Darier disease 0.364 8 1.45e-23 3.45e-22 ✓ sig.
Benign pemphigus Cutis laxa 0.364 8 1.45e-23 3.45e-22 ✓ sig.
Cutis laxa Rothmund-thomson syndrome 0.320 8 7.95e-22 1.74e-20 ✓ sig.
Accessory skin tag autosomal recessive cutis laxa type 2B 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Accessory skin tag autosomal recessive cutis laxa type 2C 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Accessory skin tag autosomal recessive cutis laxa type 2D 0.111 1 5.20e-4 1.04e-3 ✓ sig.
autosomal recessive cutis laxa type 2D Benign pemphigus 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Benign familial pemphigus Benign pemphigus 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2D Darier disease 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2C Darier disease 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2C Benign pemphigus 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2B Darier disease 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2B Benign pemphigus 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal recessive cutis laxa type 2D Rothmund-thomson syndrome 0.077 1 7.79e-4 1.39e-3 ✓ sig.
autosomal recessive cutis laxa type 2C Rothmund-thomson syndrome 0.077 1 7.79e-4 1.39e-3 ✓ sig.
autosomal recessive cutis laxa type 2B Rothmund-thomson syndrome 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Dna2-related mitochondrial dna deletion syndrome Rothmund-thomson syndrome 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Rothmund-thomson syndrome Rothmund-Thomson syndrome type 1 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Accessory skin tag Demyelinating hereditary motor and sensory neuropathy 0.100 1 1.04e-3 1.72e-3 ✓ sig.
Benign pemphigus Demyelinating hereditary motor and sensory neuropathy 0.091 1 1.17e-3 1.88e-3 ✓ sig.
Darier disease Demyelinating hereditary motor and sensory neuropathy 0.091 1 1.17e-3 1.88e-3 ✓ sig.
autosomal recessive cutis laxa type 2C Cutis laxa 0.048 1 1.30e-3 2.04e-3 ✓ sig.
autosomal recessive cutis laxa type 2B Cutis laxa 0.048 1 1.30e-3 2.04e-3 ✓ sig.
Demyelinating hereditary motor and sensory neuropathy Rothmund-thomson syndrome 0.071 1 1.56e-3 2.36e-3 ✓ sig.