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 88

12 diseases · 29 shared-gene connections
12 Diseases
25 Unique genes
0.256 Avg. similarity score
Craniometaphyseal dysplasia Most-connected disease (8 links)
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Disease Searched: Bilateral microphthalmos 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 ⇵
Craniometaphyseal dysplasia 8 8 3
Schwartz-lelek syndrome 7 7 2
Craniometadiaphyseal dysplasia 6 6 2
Palmoplantar keratoderma with congenital alopecia 6 6 1
Chondrocalcinosis 5 5 3
Hallermanns syndrome 5 5 2
Autoinflammation, panniculitis, and dermatosis syndrome 4 4 1
Calcium metabolism disorders 4 4 8
Calcium pyrophosphate deposition 4 4 2
Greither disease 4 4 4
Bilateral microphthalmos 3 3 5
Erythrokeratodermia variabilis 2 2 10

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

Gene ⇵ Member diseases ⇵ Linked diseases
GJA1 7 / 12 Bilateral microphthalmos, Craniometaphyseal dysplasia, Erythrokeratodermia variabilis, Greither disease and 3 more
ANKH 6 / 12 Calcium metabolism disorders, Calcium pyrophosphate deposition, Chondrocalcinosis, Craniometadiaphyseal dysplasia and 2 more
OTULIN 5 / 12 Autoinflammation, panniculitis, and dermatosis syndrome, Calcium metabolism disorders, Chondrocalcinosis, Craniometadiaphyseal dysplasia and 1 more
GJB3 2 / 12 Erythrokeratodermia variabilis, Greither disease
GJB4 2 / 12 Erythrokeratodermia variabilis, Greither disease
PERP 2 / 12 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 80.1× 6.37e-6 2.35e-4 ✓ sig.
Nef mediated downregulation of MHC class I complex cell surface expression
AP1B1, AP1S1
 Reactome 2 / 10 96.1× 1.85e-4 3.73e-3 ✓ sig.
Miscellaneous transport and binding events
ANKH, NIPAL4
 Reactome 2 / 25 38.4× 1.21e-3 1.61e-2 ✓ sig.
MHC class II antigen presentation
AP2S1, AP1B1, AP1S1
 Reactome 3 / 123 11.7× 2.05e-3 2.36e-2 ✓ sig.
Retinoid metabolism disease events
RBP4
 Reactome 1 / 1 480× 2.08e-3 2.39e-2 ✓ sig.
Lysosome Vesicle Biogenesis
AP1B1, AP1S1
 Reactome 2 / 35 27.5× 2.37e-3 2.64e-2 ✓ sig.
Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD)
POMC
 Reactome 1 / 2 240× 4.16e-3 3.93e-2 ✓ sig.
Peptide hormone biosynthesis
POMC
 Reactome 1 / 2 240× 4.16e-3 3.93e-2 ✓ sig.
EPH-ephrin mediated repulsion of cells
EPHA2, AP2S1
 Reactome 2 / 50 19.2× 4.79e-3 4.33e-2 ✓ sig.
Golgi Associated Vesicle Biogenesis
AP1B1, AP1S1
 Reactome 2 / 56 17.2× 5.98e-3 5.03e-2
Regulation of gap junction activity
GJA1
 Reactome 1 / 3 160× 6.23e-3 5.17e-2
Opioid Signalling
POMC
 Reactome 1 / 3 160× 6.23e-3 5.17e-2
Cortisol synthesis and secretion
GNA11, POMC
 KEGG 2 / 65 14.8× 7.99e-3 6.07e-2
Human immunodeficiency virus 1 infection
GNA11, AP1B1, AP1S1
 KEGG 3 / 213 6.8× 9.49e-3 6.77e-2
Insulin secretion
GNA11, TRPM4
 KEGG 2 / 86 11.2× 1.37e-2 8.45e-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 / 5 299× 1.71e-5 8.07e-4 ✓ sig.
skeletal system development
EPHA2, GNA11, ANKH, TNFRSF11B
 GO:0001501 4 / 151 19.8× 4.54e-5 1.71e-3 ✓ sig.
positive regulation of insulin secretion
RBP4, CASR, GNA11
 GO:0032024 3 / 60 37.4× 6.88e-5 2.34e-3 ✓ sig.
phototransduction, visible light
RBP4, GNA11
 GO:0007603 2 / 13 115× 1.33e-4 3.82e-3 ✓ sig.
cell communication
GJA1, GJB3, GJB4
 GO:0007154 3 / 80 28.0× 1.62e-4 4.43e-3 ✓ sig.
cell-cell signaling
GJA1, POMC, GJB3, GJB4
 GO:0007267 4 / 234 12.8× 2.47e-4 5.96e-3 ✓ sig.
bone remodeling
GJA1, EPHA2
 GO:0046849 2 / 18 83.1× 2.59e-4 6.18e-3 ✓ sig.
melanosome assembly
AP1B1, AP1S1
 GO:1903232 2 / 19 78.7× 2.90e-4 6.68e-3 ✓ sig.
heart development
GJA1, RBP4, GNA11, AP1B1
 GO:0007507 4 / 273 11.0× 4.43e-4 8.98e-3 ✓ sig.
platelet dense granule organization
AP1B1, AP1S1
 GO:0060155 2 / 25 59.8× 5.06e-4 9.82e-3 ✓ sig.
positive regulation of vasoconstriction
CASR, TRPM4
 GO:0045907 2 / 27 55.4× 5.91e-4 1.09e-2 ✓ sig.
transmembrane transport
GJA1, ANKH, GJB3, GJB4, TRPM4
 GO:0055085 5 / 557 6.7× 7.49e-4 1.28e-2 ✓ sig.
notochord cell development
EPHA2
 GO:0060035 1 / 1 747× 1.34e-3 1.83e-2 ✓ sig.
microtubule-based transport
GJA1
 GO:0099111 1 / 1 747× 1.34e-3 1.83e-2 ✓ sig.
regulation of melanocyte differentiation
GNA11
 GO:0045634 1 / 1 747× 1.34e-3 1.83e-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 8.97e-14 1.17e-12 ✓ sig.
Craniometaphyseal dysplasia Schwartz-lelek syndrome 0.500 2 2.53e-8 1.93e-7 ✓ sig.
Craniometadiaphyseal dysplasia Craniometaphyseal dysplasia 0.500 2 2.53e-8 1.93e-7 ✓ sig.
Chondrocalcinosis Craniometadiaphyseal dysplasia 0.500 2 2.53e-8 1.93e-7 ✓ sig.
Chondrocalcinosis Craniometaphyseal dysplasia 0.400 2 7.59e-8 5.43e-7 ✓ sig.
Calcium metabolism disorders Craniometadiaphyseal dysplasia 0.222 2 2.36e-7 1.56e-6 ✓ sig.
Calcium metabolism disorders Chondrocalcinosis 0.200 2 7.08e-7 4.28e-6 ✓ sig.
Calcium metabolism disorders Craniometaphyseal dysplasia 0.200 2 7.08e-7 4.28e-6 ✓ sig.
Palmoplantar keratoderma with congenital alopecia Schwartz-lelek syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Autoinflammation, panniculitis, and dermatosis syndrome Craniometadiaphyseal dysplasia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Hallermanns syndrome Palmoplantar keratoderma with congenital alopecia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Autoinflammation, panniculitis, and dermatosis syndrome Chondrocalcinosis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Craniometaphyseal dysplasia Palmoplantar keratoderma with congenital alopecia 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Autoinflammation, panniculitis, and dermatosis syndrome Craniometaphyseal dysplasia 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Calcium pyrophosphate deposition Schwartz-lelek syndrome 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Calcium pyrophosphate deposition Craniometadiaphyseal dysplasia 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Hallermanns syndrome Schwartz-lelek syndrome 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Craniometadiaphyseal dysplasia Schwartz-lelek syndrome 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Greither disease Palmoplantar keratoderma with congenital alopecia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Bilateral microphthalmos Palmoplantar keratoderma with congenital alopecia 0.167 1 3.25e-4 7.68e-4 ✓ sig.
Calcium pyrophosphate deposition Chondrocalcinosis 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Craniometaphyseal dysplasia Hallermanns syndrome 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Calcium pyrophosphate deposition Craniometaphyseal dysplasia 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Greither disease Hallermanns syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Greither disease Schwartz-lelek syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Autoinflammation, panniculitis, and dermatosis syndrome Calcium metabolism disorders 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Bilateral microphthalmos Hallermanns syndrome 0.143 1 6.49e-4 1.24e-3 ✓ sig.
Bilateral microphthalmos Schwartz-lelek syndrome 0.143 1 6.49e-4 1.24e-3 ✓ sig.
Erythrokeratodermia variabilis Palmoplantar keratoderma with congenital alopecia 0.091 1 6.49e-4 1.24e-3 ✓ sig.