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 142

10 diseases · 13 shared-gene connections
10 Diseases
19 Unique genes
0.184 Avg. similarity score
Skin ulcer Most-connected disease (7 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 ⇵
Skin ulcer 7 7 6
Leukocyte adhesion deficiency 4 4 3
Congenital leukocyte adherence deficiency 3 3 2
Tonic-clonic epilepsy 3 3 12
Congenital sensory neuropathy 2 2 1
Periapical periodontitis 2 2 2
leukocyte adhesion deficiency 3 2 2 1
Laryngo-onycho-cutaneous syndrome 1 1 1
Prolidase deficiency 1 1 1
leukocyte adhesion deficiency type II 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FERMT3 3 / 10 Congenital leukocyte adherence deficiency, Leukocyte adhesion deficiency, leukocyte adhesion deficiency 3
FGF2 3 / 10 Periapical periodontitis, Skin ulcer, Tonic-clonic epilepsy
ITGB2 3 / 10 Congenital leukocyte adherence deficiency, Leukocyte adhesion deficiency, Skin ulcer
NGF 3 / 10 Congenital sensory neuropathy, Skin ulcer, Tonic-clonic epilepsy
LAMA3 2 / 10 Laryngo-onycho-cutaneous syndrome, Skin ulcer
PEPD 2 / 10 Prolidase deficiency, Skin ulcer
SLC35C1 2 / 10 Leukocyte adhesion deficiency, leukocyte adhesion deficiency type II
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 ⇵
Interleukin-4 and Interleukin-13 signaling
FGF2, ITGB2, MMP9, POMC
 Reactome 4 / 108 23.4× 2.16e-5 6.37e-4 ✓ sig.
PI3K-Akt signaling pathway
FGF2, LAMA3, NGF, BDNF, NTF3
 KEGG 5 / 361 8.8× 1.96e-4 3.85e-3 ✓ sig.
Ras signaling pathway
FGF2, NGF, BDNF, NTF3
 KEGG 4 / 237 10.7× 4.54e-4 7.39e-3 ✓ sig.
Endocrine resistance
MMP9, CYP2D6, HBEGF
 KEGG 3 / 99 19.2× 4.78e-4 7.70e-3 ✓ sig.
Neurotrophin signaling pathway
NGF, BDNF, NTF3
 KEGG 3 / 120 15.8× 8.39e-4 1.19e-2 ✓ sig.
MAPK signaling pathway
FGF2, NGF, BDNF, NTF3
 KEGG 4 / 299 8.5× 1.09e-3 1.44e-2 ✓ sig.
Estrogen signaling pathway
MMP9, HBEGF, POMC
 KEGG 3 / 139 13.6× 1.28e-3 1.63e-2 ✓ sig.
Defective SLC35C1 causes congenital disorder of glycosylation 2C (CDG2C)
SLC35C1
 Reactome 1 / 1 632× 1.58e-3 1.92e-2 ✓ sig.
Bladder cancer
MMP9, HBEGF
 KEGG 2 / 41 30.8× 1.87e-3 2.17e-2 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
LAMA3, MMP9
 Reactome 2 / 51 24.8× 2.89e-3 3.00e-2 ✓ sig.
Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD)
POMC
 Reactome 1 / 2 316× 3.16e-3 3.20e-2 ✓ sig.
TRKA activation by NGF
NGF
 Reactome 1 / 2 316× 3.16e-3 3.20e-2 ✓ sig.
NFG and proNGF binds to p75NTR
NGF
 Reactome 1 / 2 316× 3.16e-3 3.20e-2 ✓ sig.
NTF3 activates NTRK3 signaling
NTF3
 Reactome 1 / 2 316× 3.16e-3 3.20e-2 ✓ sig.
Peptide hormone biosynthesis
POMC
 Reactome 1 / 2 316× 3.16e-3 3.20e-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 ⇵
nerve growth factor signaling pathway
NGF, BDNF, NTF3
 GO:0038180 3 / 14 211× 3.22e-7 3.23e-5 ✓ sig.
nerve development
NGF, BDNF, NTF3
 GO:0021675 3 / 19 155× 8.55e-7 7.29e-5 ✓ sig.
endodermal cell differentiation
ITGB2, LAMA3, MMP9
 GO:0035987 3 / 36 82.0× 6.23e-6 3.57e-4 ✓ sig.
negative regulation of neuron apoptotic process
NGF, BDNF, NES, NTF3
 GO:0043524 4 / 160 24.6× 1.81e-5 8.31e-4 ✓ sig.
positive regulation of collateral sprouting
NGF, BDNF
 GO:0048672 2 / 9 219× 3.51e-5 1.38e-3 ✓ sig.
neuron projection morphogenesis
NGF, BDNF, NTF3
 GO:0048812 3 / 70 42.2× 4.67e-5 1.71e-3 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
FGF2, NGF, HBEGF, NTF3
 GO:0051897 4 / 217 18.1× 5.98e-5 2.05e-3 ✓ sig.
positive regulation of keratinocyte migration
MMP9, HBEGF
 GO:0051549 2 / 12 164× 6.43e-5 2.17e-3 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
NGF, BDNF, NTF3
 GO:0007169 3 / 120 24.6× 2.32e-4 5.61e-3 ✓ sig.
modulation of chemical synaptic transmission
NGF, BDNF, NTF3
 GO:0050804 3 / 121 24.4× 2.38e-4 5.71e-3 ✓ sig.
leukocyte cell-cell adhesion
ITGB2, FERMT3
 GO:0007159 2 / 33 59.6× 5.08e-4 9.66e-3 ✓ sig.
regulation of heart rate
OXT, SLC8A1
 GO:0002027 2 / 39 50.4× 7.10e-4 1.21e-2 ✓ sig.
collagen catabolic process
MMP9, PEPD
 GO:0030574 2 / 41 48.0× 7.84e-4 1.29e-2 ✓ sig.
GDP-fucose import into Golgi lumen
SLC35C1
 GO:0036085 1 / 1 984× 1.02e-3 1.52e-2 ✓ sig.
cocaine metabolic process
BCHE
 GO:0050783 1 / 1 984× 1.02e-3 1.52e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital leukocyte adherence deficiency Leukocyte adhesion deficiency 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Skin ulcer Tonic-clonic epilepsy 0.118 2 8.34e-6 4.40e-5 ✓ sig.
Congenital leukocyte adherence deficiency leukocyte adhesion deficiency 3 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Leukocyte adhesion deficiency leukocyte adhesion deficiency type II 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Leukocyte adhesion deficiency leukocyte adhesion deficiency 3 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital sensory neuropathy Skin ulcer 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Laryngo-onycho-cutaneous syndrome Skin ulcer 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Prolidase deficiency Skin ulcer 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Congenital leukocyte adherence deficiency Skin ulcer 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Periapical periodontitis Skin ulcer 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Congenital sensory neuropathy Tonic-clonic epilepsy 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Leukocyte adhesion deficiency Skin ulcer 0.111 1 1.17e-3 1.88e-3 ✓ sig.
Periapical periodontitis Tonic-clonic epilepsy 0.071 1 1.56e-3 2.36e-3 ✓ sig.