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 367

7 diseases · 13 shared-gene connections
7 Diseases
10 Unique genes
0.343 Avg. similarity score
Greither disease Most-connected disease (6 links)
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Disease Searched: Erythrokeratodermia variabilis et progressiva 2 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 ⇵
Greither disease 6 6 4
Deafness, autosomal recessive 4 4 1
Erythrokeratoderma 4 4 1
Erythrokeratodermia variabilis et progressiva 1 4 4 1
Peripheral neuropathy with sensorineural hearing impairment syndrome 4 4 1
Erythrokeratodermia variabilis 2 2 10
Erythrokeratodermia variabilis et progressiva 2 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GJB3 6 / 7 Deafness, autosomal recessive, Erythrokeratoderma, Erythrokeratodermia variabilis, Erythrokeratodermia variabilis et progressiva 1 and 2 more
GJB4 3 / 7 Erythrokeratodermia variabilis, Erythrokeratodermia variabilis et progressiva 2, Greither disease
GJA1 2 / 7 Erythrokeratodermia variabilis, Greither disease
PERP 2 / 7 Erythrokeratodermia variabilis, Greither disease
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 ⇵
Gap junction assembly
GJA1, GJB3, GJB4
 Reactome 3 / 18 200× 3.37e-7 1.62e-5 ✓ sig.
Nef mediated downregulation of MHC class I complex cell surface expression
AP1B1, AP1S1
 Reactome 2 / 10 240× 2.80e-5 6.85e-4 ✓ sig.
Lysosome Vesicle Biogenesis
AP1B1, AP1S1
 Reactome 2 / 35 68.6× 3.66e-4 5.24e-3 ✓ sig.
Golgi Associated Vesicle Biogenesis
AP1B1, AP1S1
 Reactome 2 / 56 42.9× 9.38e-4 1.08e-2 ✓ sig.
Regulation of gap junction activity
GJA1
 Reactome 1 / 3 400× 2.50e-3 2.23e-2 ✓ sig.
MHC class II antigen presentation
AP1B1, AP1S1
 Reactome 2 / 123 19.5× 4.44e-3 3.37e-2 ✓ sig.
Formation of the cornified envelope
KRT83, PERP
 Reactome 2 / 130 18.5× 4.94e-3 3.64e-2 ✓ sig.
Lysosome
AP1B1, AP1S1
 KEGG 2 / 133 18.1× 5.17e-3 3.73e-2 ✓ sig.
Formation of annular gap junctions
GJA1
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
Gap junction degradation
GJA1
 Reactome 1 / 12 100× 9.95e-3 5.67e-2
TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain
PERP
 Reactome 1 / 14 85.8× 1.16e-2 6.22e-2
Human immunodeficiency virus 1 infection
AP1B1, AP1S1
 KEGG 2 / 213 11.3× 1.28e-2 6.60e-2
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane
GJA1
 Reactome 1 / 18 66.7× 1.49e-2 7.22e-2
Miscellaneous transport and binding events
NIPAL4
 Reactome 1 / 25 48.0× 2.06e-2 8.74e-2
TRP channels
TRPM4
 Reactome 1 / 28 42.9× 2.31e-2 9.30e-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 ⇵
basolateral protein secretion
AP1B1, AP1S1
 GO:0110010 2 / 5 747× 2.58e-6 1.86e-4 ✓ sig.
cell communication
GJA1, GJB3, GJB4
 GO:0007154 3 / 80 70.1× 8.87e-6 4.95e-4 ✓ sig.
melanosome assembly
AP1B1, AP1S1
 GO:1903232 2 / 19 197× 4.39e-5 1.67e-3 ✓ sig.
platelet dense granule organization
AP1B1, AP1S1
 GO:0060155 2 / 25 149× 7.68e-5 2.54e-3 ✓ sig.
transmembrane transport
GJA1, GJB3, GJB4, TRPM4
 GO:0055085 4 / 557 13.4× 1.42e-4 3.98e-3 ✓ sig.
cell-cell signaling
GJA1, GJB3, GJB4
 GO:0007267 3 / 234 24.0× 2.18e-4 5.39e-3 ✓ sig.
positive regulation of atrial cardiac muscle cell action potential
TRPM4
 GO:1903949 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization
TRPM4
 GO:1904199 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
microtubule-based transport
GJA1
 GO:0099111 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
3-keto-sphinganine metabolic process
KDSR
 GO:0006666 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
negative regulation of gonadotropin secretion
GJA1
 GO:0032277 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
positive regulation of morphogenesis of an epithelium
GJA1
 GO:1905332 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
membrane depolarization during Purkinje myocyte cell action potential
TRPM4
 GO:0086047 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
membrane depolarization during bundle of His cell action potential
TRPM4
 GO:0086048 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
positive regulation of mesodermal cell differentiation
GJA1
 GO:1905772 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Erythrokeratodermia variabilis Greither disease 0.364 4 8.76e-14 9.93e-13 ✓ sig.
Deafness, autosomal recessive Peripheral neuropathy with sensorineural hearing impairment syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive Erythrokeratoderma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive Erythrokeratodermia variabilis et progressiva 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythrokeratoderma Peripheral neuropathy with sensorineural hearing impairment syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythrokeratoderma Erythrokeratodermia variabilis et progressiva 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythrokeratodermia variabilis et progressiva 1 Peripheral neuropathy with sensorineural hearing impairment syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness, autosomal recessive Greither disease 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Erythrokeratoderma Greither disease 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Erythrokeratodermia variabilis et progressiva 1 Greither disease 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Erythrokeratodermia variabilis et progressiva 2 Greither disease 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Greither disease Peripheral neuropathy with sensorineural hearing impairment syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Erythrokeratodermia variabilis Erythrokeratodermia variabilis et progressiva 2 0.091 1 6.46e-4 1.09e-3 ✓ sig.