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 122

12 diseases · 41 shared-gene connections
12 Diseases
7 Unique genes
0.455 Avg. similarity score
Diffuse melanocytosis Most-connected disease (11 links)
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Disease Searched: Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 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 ⇵
Diffuse melanocytosis 11 11 1
Lobular capilliary hemangioma 11 11 2
Neurofibrosarcoma 11 11 1
Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 9 9 1
Sex hormone-producing adrenal cortex adenoma 9 9 2
Mediastinum angiosarcoma 5 5 3
Melanocytic naevi 5 5 2
Melanosis, neurocutaneous 5 5 1
Noonan syndrome 6 5 5 1
Ras-associated autoimmune leukoproliferative disease 5 5 2
Intradermal nevus 3 3 4
Tufted angioma 3 3 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
NRAS 12 / 12 Diffuse melanocytosis, Intradermal nevus, Lobular capilliary hemangioma, Mediastinum angiosarcoma and 8 more
KRAS 3 / 12 Intradermal nevus, Lobular capilliary hemangioma, Ras-associated autoimmune leukoproliferative disease
BRAF 2 / 12 Intradermal nevus, Melanocytic naevi
TP53 2 / 12 Mediastinum angiosarcoma, Sex hormone-producing adrenal cortex adenoma
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 ⇵
Thyroid cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 37 185× 2.65e-9 2.24e-7 ✓ sig.
Bladder cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 41 167× 4.06e-9 3.31e-7 ✓ sig.
Endometrial cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 59 116× 1.82e-8 1.25e-6 ✓ sig.
Proteoglycans in cancer
NRAS, KRAS, TP53, BRAF, KDR
 KEGG 5 / 204 42.1× 2.75e-8 1.81e-6 ✓ sig.
Central carbon metabolism in cancer
NRAS, KRAS, TP53, IDH2
 KEGG 4 / 71 96.7× 3.87e-8 2.44e-6 ✓ sig.
Melanoma
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 73 94.0× 4.34e-8 2.70e-6 ✓ sig.
Non-small cell lung cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 73 94.0× 4.34e-8 2.70e-6 ✓ sig.
VEGFR2 mediated cell proliferation
NRAS, KRAS, KDR
 Reactome 3 / 14 368× 4.40e-8 2.73e-6 ✓ sig.
Glioma
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 76 90.3× 5.11e-8 3.10e-6 ✓ sig.
Chronic myeloid leukemia
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 77 89.1× 5.39e-8 3.25e-6 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
NRAS, KRAS, BRAF, KDR
 KEGG 4 / 80 85.8× 6.29e-8 3.73e-6 ✓ sig.
Colorectal cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 87 78.9× 8.84e-8 5.01e-6 ✓ sig.
Prostate cancer
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 98 70.0× 1.43e-7 7.66e-6 ✓ sig.
Endocrine resistance
NRAS, KRAS, TP53, BRAF
 KEGG 4 / 99 69.3× 1.49e-7 7.94e-6 ✓ sig.
MAPK signaling pathway
NRAS, KRAS, TP53, BRAF, KDR
 KEGG 5 / 299 28.7× 1.87e-7 9.63e-6 ✓ 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 ⇵
Ras protein signal transduction
NRAS, KRAS, TP53
 GO:0007265 3 / 79 101× 2.51e-6 1.82e-4 ✓ sig.
negative regulation of glial cell proliferation
TP53, IDH2
 GO:0060253 2 / 11 485× 6.60e-6 3.94e-4 ✓ sig.
MAPK cascade
NRAS, KRAS, BRAF
 GO:0000165 3 / 147 54.5× 1.63e-5 7.92e-4 ✓ sig.
glial cell proliferation
KRAS, TP53
 GO:0014009 2 / 18 297× 1.84e-5 8.67e-4 ✓ sig.
negative regulation of neuron apoptotic process
KRAS, BRAF, KDR
 GO:0043524 3 / 160 50.1× 2.10e-5 9.61e-4 ✓ sig.
positive regulation of cellular senescence
KRAS, TP53
 GO:2000774 2 / 20 267× 2.28e-5 1.02e-3 ✓ sig.
negative regulation of endothelial cell apoptotic process
BRAF, KDR
 GO:2000352 2 / 39 137× 8.85e-5 2.83e-3 ✓ sig.
T cell differentiation in thymus
TP53, BRAF
 GO:0033077 2 / 41 130× 9.79e-5 3.04e-3 ✓ sig.
visual learning
KRAS, BRAF
 GO:0008542 2 / 54 98.9× 1.71e-4 4.53e-3 ✓ sig.
stem cell proliferation
TP53, KDR
 GO:0072089 2 / 54 98.9× 1.71e-4 4.53e-3 ✓ sig.
cellular response to xenobiotic stimulus
TP53, BRAF
 GO:0071466 2 / 65 82.1× 2.47e-4 5.91e-3 ✓ sig.
positive regulation of endothelial cell proliferation
NRAS, KDR
 GO:0001938 2 / 69 77.4× 2.79e-4 6.43e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 2,670× 3.75e-4 7.81e-3 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 2,670× 3.75e-4 7.81e-3 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 2,670× 3.75e-4 7.81e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Neurofibrosarcoma Noonan syndrome 6 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanocytic naevi Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanocytic naevi Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanosis, neurocutaneous Neurofibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Melanosis, neurocutaneous 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Melanosis, neurocutaneous 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanosis, neurocutaneous Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanosis, neurocutaneous Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurofibrosarcoma Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurofibrosarcoma Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Lobular capilliary hemangioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Noonan syndrome 6 Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Noonan syndrome 6 Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurofibrosarcoma Ras-associated autoimmune leukoproliferative disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Ras-associated autoimmune leukoproliferative disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Ras-associated autoimmune leukoproliferative disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ras-associated autoimmune leukoproliferative disease Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ras-associated autoimmune leukoproliferative disease Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Melanocytic naevi 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Neurofibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Diffuse melanocytosis Noonan syndrome 6 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Neurofibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Sex hormone-producing adrenal cortex adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Noonan syndrome 6 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanocytic naevi Neurofibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lobular capilliary hemangioma Melanocytic naevi 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mediastinum angiosarcoma Neurofibrosarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Diffuse melanocytosis Mediastinum angiosarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lobular capilliary hemangioma Mediastinum angiosarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intradermal nevus Lobular capilliary hemangioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Diffuse melanocytosis Intradermal nevus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intradermal nevus Neurofibrosarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mediastinum angiosarcoma Sex hormone-producing adrenal cortex adenoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mediastinum angiosarcoma Ras-associated autoimmune lymphoproliferative syndrome type iv, somatic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurofibrosarcoma Tufted angioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Diffuse melanocytosis Tufted angioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lobular capilliary hemangioma Tufted angioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.