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 420

5 diseases · 10 shared-gene connections
5 Diseases
1 Unique genes
0.500 Avg. similarity score
Bullous diffuse cutaneous mastocytosis Most-connected disease (4 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 ⇵
Bullous diffuse cutaneous mastocytosis 4 4 1
Mast cell leukemia 4 4 1
Telangiectasia macularis eruptiva perstans 4 4 1
Testicular seminoma 4 4 1
Urticaria pigmentosa 4 4 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KIT 5 / 5 Bullous diffuse cutaneous mastocytosis, Mast cell leukemia, Telangiectasia macularis eruptiva perstans, Testicular seminoma and 1 more
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 ⇵
Regulation of KIT signaling
KIT
 Reactome 1 / 14 858× 1.17e-3 1.52e-2 ✓ sig.
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
KIT
 Reactome 1 / 15 801× 1.25e-3 1.60e-2 ✓ sig.
Signaling by SCF-KIT
KIT
 Reactome 1 / 37 325× 3.08e-3 3.13e-2 ✓ sig.
Acute myeloid leukemia
KIT
 KEGG 1 / 68 177× 5.66e-3 4.75e-2 ✓ sig.
Central carbon metabolism in cancer
KIT
 KEGG 1 / 71 169× 5.91e-3 4.89e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
KIT
 Reactome 1 / 75 160× 6.24e-3 5.07e-2
PIP3 activates AKT signaling
KIT
 Reactome 1 / 93 129× 7.74e-3 5.84e-2
Hematopoietic cell lineage
KIT
 KEGG 1 / 100 120× 8.33e-3 6.12e-2
Melanogenesis
KIT
 KEGG 1 / 101 119× 8.41e-3 6.17e-2
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
KIT
 Reactome 1 / 103 117× 8.58e-3 6.25e-2
RAF/MAP kinase cascade
KIT
 Reactome 1 / 124 96.9× 1.03e-2 7.01e-2
Breast cancer
KIT
 KEGG 1 / 148 81.1× 1.23e-2 7.75e-2
Phospholipase D signaling pathway
KIT
 KEGG 1 / 149 80.6× 1.24e-2 7.78e-2
Rap1 signaling pathway
KIT
 KEGG 1 / 211 56.9× 1.76e-2 9.59e-2
Ras signaling pathway
KIT
 KEGG 1 / 237 50.7× 1.97e-2 1.02e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
melanocyte adhesion
KIT
 GO:0097326 1 / 1 18,687× 5.35e-5 1.89e-3 ✓ sig.
positive regulation of pyloric antrum smooth muscle contraction
KIT
 GO:0120072 1 / 1 18,687× 5.35e-5 1.89e-3 ✓ sig.
positive regulation of colon smooth muscle contraction
KIT
 GO:1904343 1 / 1 18,687× 5.35e-5 1.89e-3 ✓ sig.
Kit signaling pathway
KIT
 GO:0038109 1 / 3 6,229× 1.61e-4 4.31e-3 ✓ sig.
melanocyte migration
KIT
 GO:0097324 1 / 3 6,229× 1.61e-4 4.31e-3 ✓ sig.
regulation of bile acid metabolic process
KIT
 GO:1904251 1 / 3 6,229× 1.61e-4 4.31e-3 ✓ sig.
positive regulation of small intestine smooth muscle contraction
KIT
 GO:1904349 1 / 3 6,229× 1.61e-4 4.31e-3 ✓ sig.
mast cell chemotaxis
KIT
 GO:0002551 1 / 4 4,672× 2.14e-4 5.28e-3 ✓ sig.
mast cell differentiation
KIT
 GO:0060374 1 / 4 4,672× 2.14e-4 5.28e-3 ✓ sig.
hematopoietic stem cell migration
KIT
 GO:0035701 1 / 4 4,672× 2.14e-4 5.28e-3 ✓ sig.
positive regulation of vascular associated smooth muscle cell differentiation
KIT
 GO:1905065 1 / 4 4,672× 2.14e-4 5.28e-3 ✓ sig.
positive regulation of mast cell cytokine production
KIT
 GO:0032765 1 / 5 3,737× 2.68e-4 6.20e-3 ✓ sig.
mast cell proliferation
KIT
 GO:0070662 1 / 5 3,737× 2.68e-4 6.20e-3 ✓ sig.
positive regulation of dendritic cell cytokine production
KIT
 GO:0002732 1 / 5 3,737× 2.68e-4 6.20e-3 ✓ sig.
positive regulation of mast cell proliferation
KIT
 GO:0070668 1 / 5 3,737× 2.68e-4 6.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bullous diffuse cutaneous mastocytosis Mast cell leukemia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Bullous diffuse cutaneous mastocytosis Telangiectasia macularis eruptiva perstans 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Bullous diffuse cutaneous mastocytosis Testicular seminoma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Bullous diffuse cutaneous mastocytosis Urticaria pigmentosa 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Mast cell leukemia Telangiectasia macularis eruptiva perstans 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Mast cell leukemia Testicular seminoma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Mast cell leukemia Urticaria pigmentosa 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Telangiectasia macularis eruptiva perstans Testicular seminoma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Telangiectasia macularis eruptiva perstans Urticaria pigmentosa 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Testicular seminoma Urticaria pigmentosa 0.500 1 6.49e-5 2.34e-4 ✓ sig.