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 126

10 diseases · 13 shared-gene connections
10 Diseases
31 Unique genes
0.226 Avg. similarity score
Headache Most-connected disease (5 links)
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Disease Searched: Angiolymphoid hyperplasia 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 ⇵
Headache 5 5 10
Angiofollicular ganglionic hyperplasia 4 4 1
Angiolymphoid hyperplasia 4 4 1
Castleman disease 4 4 1
Intracranial arteriovenous malformation 3 3 3
Pleural diseases 2 2 10
Congenital microtia 1 1 1
Endometrioid carcinoma 1 1 1
Occupational disease 1 1 13
short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IL6 6 / 10 Angiofollicular ganglionic hyperplasia, Angiolymphoid hyperplasia, Castleman disease, Headache and 2 more
CARD8 2 / 10 Occupational disease, Pleural diseases
MSLN 2 / 10 Endometrioid carcinoma, Pleural diseases
PRKRA 2 / 10 Congenital microtia, Headache
SLC10A7 2 / 10 Headache, short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis
TGFB1 2 / 10 Occupational disease, Pleural diseases
TIMP2 2 / 10 Occupational disease, Pleural diseases
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 ⇵
Malaria
IL6, CSF3, TGFB1, CCL2, IFNG
 KEGG 5 / 50 38.7× 1.60e-7 1.05e-5 ✓ sig.
Cytokine-cytokine receptor interaction
IL6, CSF3, IFNA2, TGFB1, CCL2, CXCR3, IFNG, IL4
 KEGG 8 / 298 10.4× 6.28e-7 3.47e-5 ✓ sig.
IL-17 signaling pathway
IL6, CSF3, CCL2, IFNG, IL4
 KEGG 5 / 94 20.6× 3.82e-6 1.64e-4 ✓ sig.
Inflammatory bowel disease
IL6, TGFB1, IFNG, IL4
 KEGG 4 / 66 23.5× 2.34e-5 7.20e-4 ✓ sig.
JAK-STAT signaling pathway
IL6, CSF3, IFNA2, IFNG, IL4
 KEGG 5 / 168 11.5× 6.39e-5 1.62e-3 ✓ sig.
Rheumatoid arthritis
IL6, TGFB1, CCL2, IFNG
 KEGG 4 / 95 16.3× 9.81e-5 2.29e-3 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
IL6, KRAS, TGFB1, CCL2
 KEGG 4 / 101 15.3× 1.25e-4 2.76e-3 ✓ sig.
Chagas disease
IL6, TGFB1, CCL2, IFNG
 KEGG 4 / 103 15.0× 1.34e-4 2.93e-3 ✓ sig.
Post-translational protein phosphorylation
IL6, MSLN, ALB, TNC
 Reactome 4 / 108 14.3× 1.61e-4 3.39e-3 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
IL6, TGFB1, CCL2, IL4
 Reactome 4 / 108 14.3× 1.61e-4 3.39e-3 ✓ sig.
Th17 cell differentiation
IL6, TGFB1, IFNG, IL4
 KEGG 4 / 109 14.2× 1.67e-4 3.49e-3 ✓ sig.
Lipid and atherosclerosis
IL6, IFNA2, KRAS, CYP1A1, CCL2
 KEGG 5 / 216 9.0× 2.08e-4 4.14e-3 ✓ sig.
RUNX3 regulates p14-ARF
KRAS, TGFB1
 Reactome 2 / 9 86.1× 2.30e-4 4.47e-3 ✓ sig.
Interleukin-10 signaling
IL6, CSF3, CCL2
 Reactome 3 / 47 24.7× 2.34e-4 4.53e-3 ✓ sig.
PI3K-Akt signaling pathway
IL6, CSF3, IFNA2, KRAS, IL4, TNC
 KEGG 6 / 361 6.4× 2.76e-4 5.15e-3 ✓ 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 ⇵
humoral immune response
IL6, IFNA2, CCL2, IFNG
 GO:0006959 4 / 58 41.6× 2.47e-6 1.77e-4 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT
IL6, CCL2, IFNG, IL4
 GO:0007259 4 / 67 36.0× 4.41e-6 2.79e-4 ✓ sig.
response to genistein
OXT, CYP1A1
 GO:0033595 2 / 3 402× 7.98e-6 4.53e-4 ✓ sig.
female pregnancy
GNRH1, OXT, KRAS, TGFB1
 GO:0007565 4 / 80 30.1× 8.97e-6 4.98e-4 ✓ sig.
response to toxic substance
TTPA, CYP1A1, NQO1, PON1
 GO:0009636 4 / 83 29.1× 1.04e-5 5.56e-4 ✓ sig.
cell surface receptor signaling pathway via STAT
IL6, IFNA2, IFNG
 GO:0097696 3 / 28 64.6× 1.32e-5 6.69e-4 ✓ sig.
cellular response to virus
IL6, IFNA2, TGFB1, IFNG
 GO:0098586 4 / 89 27.1× 1.37e-5 6.92e-4 ✓ sig.
positive regulation of gene expression
IL6, KRAS, TGFB1, CCL2, IFNG, IL4, TNC
 GO:0010628 7 / 504 8.4× 1.49e-5 7.38e-4 ✓ sig.
positive regulation of cell population proliferation
IL6, CSF3, TGFB1, CXCR3, IFNG, IL4, TNC
 GO:0008284 7 / 532 7.9× 2.12e-5 9.69e-4 ✓ sig.
response to food
OXT, CYP1A1, MPO
 GO:0032094 3 / 33 54.8× 2.18e-5 9.92e-4 ✓ sig.
digestive tract development
NIPBL, CYP1A1, TGFB1
 GO:0048565 3 / 34 53.2× 2.39e-5 1.06e-3 ✓ sig.
immune response
IL6, PRKRA, CSF3, CCL2, CXCR3, IFNG, IL4
 GO:0006955 7 / 543 7.8× 2.41e-5 1.07e-3 ✓ sig.
vitamin E metabolic process
TTPA, NQO1
 GO:0042360 2 / 5 241× 2.66e-5 1.15e-3 ✓ sig.
response to ethanol
CSF3, GNRH1, TGFB1, TNC
 GO:0045471 4 / 110 21.9× 3.16e-5 1.31e-3 ✓ sig.
coumarin metabolic process
CYP1A1, CYP2D6
 GO:0009804 2 / 7 172× 5.56e-5 2.02e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Occupational disease Pleural diseases 0.143 3 5.62e-8 4.10e-7 ✓ sig.
Angiofollicular ganglionic hyperplasia Angiolymphoid hyperplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Angiofollicular ganglionic hyperplasia Castleman disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Angiolymphoid hyperplasia Castleman disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Angiofollicular ganglionic hyperplasia Intracranial arteriovenous malformation 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Angiolymphoid hyperplasia Intracranial arteriovenous malformation 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Castleman disease Intracranial arteriovenous malformation 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital microtia Headache 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Endometrioid carcinoma Pleural diseases 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Angiofollicular ganglionic hyperplasia Headache 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Angiolymphoid hyperplasia Headache 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Castleman disease Headache 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Headache short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis 0.091 1 6.49e-4 1.24e-3 ✓ sig.