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 289

6 diseases · 9 shared-gene connections
6 Diseases
58 Unique genes
0.135 Avg. similarity score
Cervical disc degenerative disorder Most-connected disease (5 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 ⇵
Cervical disc degenerative disorder 5 5 6
Intervertebral disc disease 5 5 10
Berylliosis 2 2 10
Gouty arthritis 2 2 15
Trigeminal neuralgia 2 2 12
Uremia 2 2 18

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

Gene ⇵ Member diseases ⇵ Linked diseases
TGFB1 5 / 6 Berylliosis, Cervical disc degenerative disorder, Gouty arthritis, Intervertebral disc disease and 1 more
IL1B 4 / 6 Cervical disc degenerative disorder, Gouty arthritis, Intervertebral disc disease, Trigeminal neuralgia
TNF 4 / 6 Berylliosis, Cervical disc degenerative disorder, Intervertebral disc disease, Trigeminal neuralgia
SPARC 3 / 6 Cervical disc degenerative disorder, Intervertebral disc disease, Uremia
ASPN 2 / 6 Cervical disc degenerative disorder, Intervertebral disc 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 ⇵
AGE-RAGE signaling pathway in diabetic complications
IL1B, TGFB1, IL6, TNF, COL1A1, MAPK1, MAPK3, MAPK8, MAPK9, ICAM1, NOS3, TGFBR1
 KEGG 13 / 101 26.7× 1.10e-15 4.22e-13 ✓ sig.
Th17 cell differentiation
IL1B, TGFB1, HLA-DPB1, HLA-DRB1, IL2RA, IL6, FOS, MAPK1, MAPK3, MAPK8, MAPK9, TGFBR1
 KEGG 12 / 109 22.8× 1.06e-13 2.69e-11 ✓ sig.
Rheumatoid arthritis
IL1B, TGFB1, CD28, HLA-DPB1, HLA-DRB1, IL6, TNF, FOS, FLT1, ICAM1, PTH
 KEGG 11 / 95 24.0× 7.02e-13 1.58e-10 ✓ sig.
Chagas disease
IL1B, TGFB1, ACE, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, TGFBR1
 KEGG 11 / 103 22.1× 1.74e-12 3.65e-10 ✓ sig.
Human T-cell leukemia virus 1 infection
TGFB1, HLA-DPB1, HLA-DRB1, IL2RA, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, ICAM1
 KEGG 13 / 224 12.0× 3.51e-11 5.59e-9 ✓ sig.
Tuberculosis
CD14, IL1B, TGFB1, HLA-DPB1, HLA-DRB1, IL6, TNF, MAPK1, MAPK3, MAPK8, MAPK9, VDR
 KEGG 12 / 181 13.7× 4.65e-11 7.23e-9 ✓ sig.
Toll-like receptor signaling pathway
CD14, IL1B, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, SPP1
 KEGG 10 / 109 19.0× 9.04e-11 1.31e-8 ✓ sig.
Pertussis
CD14, IL1B, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9
 KEGG 9 / 78 23.9× 1.05e-10 1.51e-8 ✓ sig.
Focal adhesion
COL1A1, COL9A3, THBS2, COL9A2, MAPK1, MAPK3, MAPK8, MAPK9, PRKCG, FLT1, KDR, SPP1
 KEGG 12 / 203 12.2× 1.77e-10 2.43e-8 ✓ sig.
TNF signaling pathway
IL1B, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, ICAM1, VCAM1
 KEGG 10 / 119 17.4× 2.18e-10 2.91e-8 ✓ sig.
Lipid and atherosclerosis
CD14, IL1B, IL6, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, ICAM1, NOS3, VCAM1
 KEGG 12 / 216 11.5× 3.64e-10 4.58e-8 ✓ sig.
Activation of the AP-1 family of transcription factors
FOS, MAPK1, MAPK3, MAPK8, MAPK9
 Reactome 5 / 10 104× 5.45e-10 6.56e-8 ✓ sig.
PI3K-Akt signaling pathway
IL2RA, IL6, COL1A1, COL9A3, THBS2, COL9A2, MAPK1, MAPK3, EPO, FLT1, KDR, NOS3
 KEGG 14 / 361 8.0× 1.17e-9 1.28e-7 ✓ sig.
Osteoclast differentiation
IL1B, TGFB1, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, TGFBR1, TNFRSF11B
 KEGG 10 / 142 14.6× 1.25e-9 1.36e-7 ✓ sig.
MAPK signaling pathway
CD14, IL1B, TGFB1, TNF, FOS, MAPK1, MAPK3, MAPK8, MAPK9, PRKCG, FLT1, KDR
 KEGG 13 / 299 9.0× 1.26e-9 1.36e-7 ✓ 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 ⇵
positive regulation of T cell proliferation
IL1B, BTNL2, CD28, HLA-DPB1, IL2RA, IL6, AIF1, VCAM1
 GO:0042102 8 / 67 38.5× 2.95e-11 9.58e-9 ✓ sig.
positive regulation of neuroinflammatory response
IL1B, IL6, TNF, MAPK1, MAPK3
 GO:0150078 5 / 16 101× 1.03e-9 2.29e-7 ✓ sig.
positive regulation of gene expression
IL1B, TGFB1, CD28, IL6, TNF, MAPK8, MAPK9, BMP2, NOS3, PTH, RUNX2, TGFBR1
 GO:0010628 13 / 504 8.3× 3.57e-9 6.91e-7 ✓ sig.
positive regulation of ERK1 and ERK2 cascade
IL1B, TGFB1, HLA-DRB1, TNF, MAPK3, BMP2, EPO, ICAM1, KDR
 GO:0070374 9 / 201 14.4× 1.09e-8 1.84e-6 ✓ sig.
inflammatory response
CD14, HP, IL1B, IL1RN, TGFB1, IL2RA, IL6, TNF, AIF1, FOS, BMP2, VCAM1
 GO:0006954 12 / 467 8.3× 1.62e-8 2.60e-6 ✓ sig.
skeletal system development
COL1A1, COL9A2, BMP2, PTH, RUNX2, TGFBR1, TNFRSF11B, VDR
 GO:0001501 8 / 151 17.1× 2.05e-8 3.20e-6 ✓ sig.
positive regulation of epithelial to mesenchymal transition
IL1B, TGFB1, IL6, COL1A1, BMP2, TGFBR1
 GO:0010718 6 / 59 32.8× 2.72e-8 4.06e-6 ✓ sig.
positive regulation of MAPK cascade
ADRB3, IL1B, TGFB1, HLA-DRB1, IL6, TNF, BMP2, FLT1, KDR
 GO:0043410 9 / 224 12.9× 2.78e-8 4.12e-6 ✓ sig.
response to lipopolysaccharide
IL1B, TNF, FOS, MAPK1, MAPK3, EPO, NOS3, VCAM1
 GO:0032496 8 / 161 16.0× 3.39e-8 4.87e-6 ✓ sig.
positive regulation of mononuclear cell migration
TGFB1, TNF, AIF1
 GO:0071677 3 / 4 242× 1.13e-7 1.34e-5 ✓ sig.
regulation of blood pressure
POMC, ACE, CALCA, COMT, NOS3, SGK1
 GO:0008217 6 / 83 23.3× 2.15e-7 2.31e-5 ✓ sig.
embryo implantation
A1CF, IL1B, CALCA, EPO, SPP1
 GO:0007566 5 / 48 33.6× 3.73e-7 3.66e-5 ✓ sig.
vascular endothelial growth factor production
IL1B, IL6, TNF
 GO:0010573 3 / 6 161× 5.64e-7 5.18e-5 ✓ sig.
positive regulation of glial cell proliferation
IL1B, IL6, TNF, GFAP
 GO:0060252 4 / 22 58.6× 5.86e-7 5.35e-5 ✓ sig.
positive regulation of miRNA transcription
TGFB1, IL6, TNF, FOS, BMP2
 GO:1902895 5 / 56 28.8× 8.17e-7 7.05e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cervical disc degenerative disorder Intervertebral disc disease 0.417 5 2.10e-16 3.49e-15 ✓ sig.
Berylliosis Cervical disc degenerative disorder 0.133 2 5.69e-6 3.09e-5 ✓ sig.
Cervical disc degenerative disorder Trigeminal neuralgia 0.118 2 8.34e-6 4.40e-5 ✓ sig.
Cervical disc degenerative disorder Gouty arthritis 0.100 2 1.33e-5 6.83e-5 ✓ sig.
Berylliosis Intervertebral disc disease 0.105 2 1.70e-5 8.62e-5 ✓ sig.
Cervical disc degenerative disorder Uremia 0.087 2 1.93e-5 9.70e-5 ✓ sig.
Intervertebral disc disease Trigeminal neuralgia 0.095 2 2.50e-5 1.23e-4 ✓ sig.
Gouty arthritis Intervertebral disc disease 0.083 2 3.97e-5 1.92e-4 ✓ sig.
Intervertebral disc disease Uremia 0.074 2 5.78e-5 2.34e-4 ✓ sig.