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 178

10 diseases · 27 shared-gene connections
10 Diseases
11 Unique genes
0.338 Avg. similarity score
Familial multiple nevi flammei Most-connected disease (8 links)
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Disease Searched: Sturge-weber syndrome 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 ⇵
Familial multiple nevi flammei 8 8 1
Hemangioma of choroid 8 8 1
Melanocytoma of the eyeball 8 8 1
Sturge-weber syndrome 8 8 1
Sturge-weber syndrome, somatic, mosaic 5 5 2
Blood vessel neoplasm 4 4 5
Conjunctival nevus 4 4 3
Malignant myoepithelioma 4 4 3
Port-wine stain 4 4 2
Neurodevelopmental disorder with hypotonia and dysmorphic facies 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GNAQ 9 / 10 Blood vessel neoplasm, Conjunctival nevus, Familial multiple nevi flammei, Hemangioma of choroid and 5 more
GNB2 2 / 10 Neurodevelopmental disorder with hypotonia and dysmorphic facies, Sturge-weber syndrome, somatic, mosaic
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 ⇵
Hepatocellular carcinoma
NRAS, PIK3CA, CDKN2A, SMARCB1, BRAF
 KEGG 5 / 170 32.1× 2.31e-7 1.17e-5 ✓ sig.
Melanoma
NRAS, PIK3CA, CDKN2A, BRAF
 KEGG 4 / 73 59.8× 4.01e-7 1.89e-5 ✓ sig.
Non-small cell lung cancer
NRAS, PIK3CA, CDKN2A, BRAF
 KEGG 4 / 73 59.8× 4.01e-7 1.89e-5 ✓ sig.
Chemokine signaling pathway
GNAQ, NRAS, PIK3CA, BRAF, GNB2
 KEGG 5 / 193 28.3× 4.35e-7 2.02e-5 ✓ sig.
Glioma
NRAS, PIK3CA, CDKN2A, BRAF
 KEGG 4 / 76 57.5× 4.72e-7 2.18e-5 ✓ sig.
Chronic myeloid leukemia
NRAS, PIK3CA, CDKN2A, BRAF
 KEGG 4 / 77 56.7× 4.98e-7 2.28e-5 ✓ sig.
Human cytomegalovirus infection
GNAQ, NRAS, PIK3CA, CDKN2A, GNB2
 KEGG 5 / 226 24.2× 9.51e-7 4.00e-5 ✓ sig.
Endocrine resistance
NRAS, PIK3CA, CDKN2A, BRAF
 KEGG 4 / 99 44.1× 1.37e-6 5.49e-5 ✓ sig.
Downstream signal transduction
RASA1, NRAS, PIK3CA
 Reactome 3 / 29 113× 2.06e-6 7.76e-5 ✓ sig.
Cholinergic synapse
GNAQ, NRAS, PIK3CA, GNB2
 KEGG 4 / 115 38.0× 2.50e-6 9.13e-5 ✓ sig.
Serotonergic synapse
GNAQ, NRAS, BRAF, GNB2
 KEGG 4 / 115 38.0× 2.50e-6 9.13e-5 ✓ sig.
Pathways in cancer
GNAQ, NRAS, PIK3CA, CDKN2A, BRAF, GNB2
 KEGG 6 / 533 12.3× 2.84e-6 1.02e-4 ✓ sig.
Bladder cancer
NRAS, CDKN2A, BRAF
 KEGG 3 / 41 79.9× 5.98e-6 1.91e-4 ✓ sig.
Endometrial cancer
NRAS, PIK3CA, BRAF
 KEGG 3 / 59 55.5× 1.81e-5 4.79e-4 ✓ sig.
Long-term depression
GNAQ, NRAS, BRAF
 KEGG 3 / 60 54.6× 1.90e-5 5.00e-4 ✓ 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 ⇵
autosome genomic imprinting
DNMT3A, PIK3CA
 GO:0141068 2 / 6 566× 4.72e-6 3.03e-4 ✓ sig.
negative regulation of cell-matrix adhesion
RASA1, CDKN2A
 GO:0001953 2 / 22 154× 7.23e-5 2.43e-3 ✓ sig.
negative regulation of neuron apoptotic process
RASA1, PIK3CA, BRAF
 GO:0043524 3 / 160 31.9× 9.66e-5 3.01e-3 ✓ sig.
regulation of canonical Wnt signaling pathway
GNAQ, AMER1
 GO:0060828 2 / 37 91.8× 2.07e-4 5.22e-3 ✓ sig.
adipose tissue development
AMER1, PIK3CA
 GO:0060612 2 / 46 73.9× 3.21e-4 7.05e-3 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
CDKN2A, SMARCB1
 GO:2000045 2 / 57 59.6× 4.94e-4 9.41e-3 ✓ sig.
single stranded viral RNA replication via double stranded DNA intermediate
SMARCB1
 GO:0039692 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
response to butyrate
PIK3CA
 GO:1903544 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
epidermal growth factor receptor signaling pathway
PIK3CA, BRAF
 GO:0007173 2 / 64 53.1× 6.23e-4 1.10e-2 ✓ sig.
somatic stem cell population maintenance
CDKN2A, BRAF
 GO:0035019 2 / 64 53.1× 6.23e-4 1.10e-2 ✓ sig.
Ras protein signal transduction
NRAS, CDKN2A
 GO:0007265 2 / 79 43.0× 9.47e-4 1.42e-2 ✓ sig.
mesenchymal cell differentiation involved in kidney development
AMER1
 GO:0072161 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
response to muscle inactivity
PIK3CA
 GO:0014870 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
regulation of gene expression
DNMT3A, PIK3CA, CDKN2A
 GO:0010468 3 / 402 12.7× 1.43e-3 1.79e-2 ✓ sig.
positive T cell selection
BRAF
 GO:0043368 1 / 3 566× 1.76e-3 1.99e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Melanocytoma of the eyeball Sturge-weber syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial multiple nevi flammei Melanocytoma of the eyeball 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial multiple nevi flammei Sturge-weber syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial multiple nevi flammei Hemangioma of choroid 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hemangioma of choroid Melanocytoma of the eyeball 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hemangioma of choroid Sturge-weber syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hemangioma of choroid Sturge-weber syndrome, somatic, mosaic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Sturge-weber syndrome Sturge-weber syndrome, somatic, mosaic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanocytoma of the eyeball Sturge-weber syndrome, somatic, mosaic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial multiple nevi flammei Sturge-weber syndrome, somatic, mosaic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Port-wine stain Sturge-weber syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodevelopmental disorder with hypotonia and dysmorphic facies Sturge-weber syndrome, somatic, mosaic 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanocytoma of the eyeball Port-wine stain 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hemangioma of choroid Port-wine stain 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial multiple nevi flammei Port-wine stain 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Conjunctival nevus Hemangioma of choroid 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Conjunctival nevus Sturge-weber syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Conjunctival nevus Melanocytoma of the eyeball 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Conjunctival nevus Familial multiple nevi flammei 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial multiple nevi flammei Malignant myoepithelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Malignant myoepithelioma Melanocytoma of the eyeball 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Malignant myoepithelioma Sturge-weber syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hemangioma of choroid Malignant myoepithelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blood vessel neoplasm Hemangioma of choroid 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blood vessel neoplasm Sturge-weber syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blood vessel neoplasm Melanocytoma of the eyeball 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blood vessel neoplasm Familial multiple nevi flammei 0.200 1 2.58e-4 5.38e-4 ✓ sig.