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 237

7 diseases · 14 shared-gene connections
7 Diseases
91 Unique genes
0.092 Avg. similarity score
Cutaneous mastocytosis 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 ⇵
Cutaneous mastocytosis 5 5 17
Mastocytosis 5 5 28
Secondary malignant neoplasm 5 5 19
Systemic mastocytosis 5 5 23
Sickle cell anemia 4 4 28
Intellectual developmental disorder growth seizures 3 3 1
isovaleric acidemia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HBE1 5 / 7 Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more
HBG2 5 / 7 Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more
OR51B5 5 / 7 Cutaneous mastocytosis, Mastocytosis, Secondary malignant neoplasm, Sickle cell anemia and 1 more
ABCA2 4 / 7 Cutaneous mastocytosis, Intellectual developmental disorder growth seizures, Mastocytosis, Systemic mastocytosis
KIT 3 / 7 Cutaneous mastocytosis, Mastocytosis, Systemic mastocytosis
OR51Q1 3 / 7 Cutaneous mastocytosis, Mastocytosis, Systemic mastocytosis
CLIC1 2 / 7 Mastocytosis, Systemic mastocytosis
CYP2B6 2 / 7 Cutaneous mastocytosis, Mastocytosis
IVD 2 / 7 isovaleric acidemia, Secondary malignant neoplasm
MOCS1 2 / 7 Mastocytosis, Systemic mastocytosis
MSH5 2 / 7 Mastocytosis, Systemic mastocytosis
PDE4DIP 2 / 7 Cutaneous mastocytosis, Mastocytosis
RPTN 2 / 7 Cutaneous mastocytosis, Mastocytosis
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 ⇵
Pyrimidine biosynthesis
CAD, DHODH, UMPS
 Reactome 3 / 3 132× 4.21e-7 2.31e-5 ✓ sig.
Biosynthesis of cofactors
ALAD, CAD, DHODH, GCH1, HMBS, UMPS, MOCS1
 KEGG 7 / 154 6.0× 1.63e-4 3.33e-3 ✓ sig.
Alternative complement activation
C3, CFB
 Reactome 2 / 5 52.8× 5.59e-4 8.69e-3 ✓ sig.
Fluid shear stress and atherosclerosis
GSTT1, NFE2L2, NOS3, TNF, VCAM1, HMOX1
 KEGG 6 / 141 5.6× 6.92e-4 1.03e-2 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
NOS3, TNF, VCAM1, VEGFC, COL4A3
 KEGG 5 / 101 6.5× 9.99e-4 1.35e-2 ✓ sig.
Lipid and atherosclerosis
APOB, NFE2L2, NOS3, TNF, VCAM1, CYP2B6, ABCA1
 KEGG 7 / 216 4.3× 1.24e-3 1.60e-2 ✓ sig.
Activation of C3 and C5
C3, CFB
 Reactome 2 / 8 33.0× 1.54e-3 1.89e-2 ✓ sig.
African trypanosomiasis
HBB, TNF, VCAM1
 KEGG 3 / 37 10.7× 2.71e-3 2.87e-2 ✓ sig.
CYP2E1 reactions
CYP2C19, CYP2B6
 Reactome 2 / 11 24.0× 2.99e-3 3.07e-2 ✓ sig.
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
GCH1, NOS3
 Reactome 2 / 11 24.0× 2.99e-3 3.07e-2 ✓ sig.
Scavenging of heme from plasma
HBB, HP
 Reactome 2 / 13 20.3× 4.19e-3 3.90e-2 ✓ sig.
Heme biosynthesis
ALAD, HMBS
 Reactome 2 / 14 18.9× 4.87e-3 4.32e-2 ✓ sig.
Porphyrin metabolism
ALAD, HMBS, HMOX1
 KEGG 3 / 46 8.6× 5.05e-3 4.40e-2 ✓ sig.
Malaria
HBB, TNF, VCAM1
 KEGG 3 / 50 7.9× 6.38e-3 5.14e-2
Pyrimidine metabolism
CAD, DHODH, UMPS
 KEGG 3 / 58 6.8× 9.61e-3 6.71e-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 ⇵
'de novo' UMP biosynthetic process
CAD, DHODH, UMPS
 GO:0044205 3 / 3 205× 1.12e-7 1.32e-5 ✓ sig.
UDP biosynthetic process
CAD, DHODH, UMPS
 GO:0006225 3 / 5 123× 1.11e-6 9.01e-5 ✓ sig.
system process
NPPB, OR51B5, OR51Q1, OR51I2, OR51L1
 GO:0003008 5 / 41 25.0× 1.60e-6 1.21e-4 ✓ sig.
'de novo' pyrimidine nucleobase biosynthetic process
CAD, DHODH, UMPS
 GO:0006207 3 / 6 103× 2.21e-6 1.56e-4 ✓ sig.
pyrimidine nucleotide biosynthetic process
CAD, DHODH, UMPS
 GO:0006221 3 / 9 68.5× 9.19e-6 4.89e-4 ✓ sig.
response to vitamin B2
MTHFR, CEBPA
 GO:0033274 2 / 2 205× 2.35e-5 1.01e-3 ✓ sig.
smooth muscle hyperplasia
NOS3, HMOX1
 GO:0014806 2 / 2 205× 2.35e-5 1.01e-3 ✓ sig.
response to xenobiotic stimulus
ALAD, GPX1, MTHFR, NFE2L2, TNF, ABCA2, VEGFC, ABCA1
 GO:0009410 8 / 248 6.6× 2.83e-5 1.17e-3 ✓ sig.
carbon dioxide transport
HBB, HBE1, HBG2
 GO:0015670 3 / 13 47.4× 3.08e-5 1.25e-3 ✓ sig.
cellular response to lipid
OR51B5, OR51Q1, OR51I2, OR51L1
 GO:0071396 4 / 38 21.6× 3.42e-5 1.35e-3 ✓ sig.
response to hydrogen peroxide
GPX1, HBB, HP, HMOX1
 GO:0042542 4 / 39 21.1× 3.80e-5 1.46e-3 ✓ sig.
oxygen transport
HBB, HBE1, HBG2
 GO:0015671 3 / 17 36.2× 7.23e-5 2.38e-3 ✓ sig.
negative regulation of systemic arterial blood pressure
NPPB, TNF, ARHGAP42
 GO:0003085 3 / 18 34.2× 8.65e-5 2.71e-3 ✓ sig.
vasodilation
GPX1, NOS3, NPPB, TNF
 GO:0042311 4 / 50 16.4× 1.02e-4 3.07e-3 ✓ sig.
positive regulation of protein-containing complex assembly
TNF, TRABD2B, FNIP2, NRG1
 GO:0031334 4 / 50 16.4× 1.02e-4 3.07e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cutaneous mastocytosis Mastocytosis 0.243 9 1.24e-21 2.70e-20 ✓ sig.
Mastocytosis Systemic mastocytosis 0.209 9 4.15e-20 8.42e-19 ✓ sig.
Cutaneous mastocytosis Systemic mastocytosis 0.171 6 6.69e-14 9.27e-13 ✓ sig.
Cutaneous mastocytosis Secondary malignant neoplasm 0.088 3 1.07e-6 6.61e-6 ✓ sig.
Secondary malignant neoplasm Systemic mastocytosis 0.075 3 2.78e-6 1.59e-5 ✓ sig.
Cutaneous mastocytosis Sickle cell anemia 0.070 3 3.60e-6 2.03e-5 ✓ sig.
Mastocytosis Secondary malignant neoplasm 0.067 3 5.12e-6 2.80e-5 ✓ sig.
Secondary malignant neoplasm Sickle cell anemia 0.067 3 5.12e-6 2.80e-5 ✓ sig.
Sickle cell anemia Systemic mastocytosis 0.061 3 9.31e-6 4.89e-5 ✓ sig.
Mastocytosis Sickle cell anemia 0.056 3 1.71e-5 8.66e-5 ✓ sig.
Cutaneous mastocytosis Intellectual developmental disorder growth seizures 0.056 1 1.10e-3 1.81e-3 ✓ sig.
isovaleric acidemia Secondary malignant neoplasm 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Intellectual developmental disorder growth seizures Systemic mastocytosis 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Intellectual developmental disorder growth seizures Mastocytosis 0.034 1 1.82e-3 2.66e-3 ✓ sig.