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 131

11 diseases · 31 shared-gene connections
11 Diseases
17 Unique genes
0.386 Avg. similarity score
Congenital hemangioma Most-connected disease (9 links)
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Disease Searched: Primary melanocytic lesion of meninges 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 ⇵
Congenital hemangioma 9 9 3
Nevus of ota 9 9 2
Primary melanocytic lesion of meninges 7 7 4
Anastomosing hemangioma 6 6 3
Meningeal melanocytoma 6 6 8
Phakomatosis pigmentovascularis 6 6 2
Capillary malformation 5 5 4
Cutis marmorata telangiectatica congenita 4 4 2
Hypercalcemia, type ii 4 4 1
Hypocalcemia, autosomal dominant 2 4 4 1
Benign blood vessel neoplasm 2 2 6

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

Gene ⇵ Member diseases ⇵ Linked diseases
GNA11 10 / 11 Anastomosing hemangioma, Capillary malformation, Congenital hemangioma, Cutis marmorata telangiectatica congenita and 6 more
GNAQ 8 / 11 Anastomosing hemangioma, Benign blood vessel neoplasm, Capillary malformation, Congenital hemangioma and 4 more
SF3B1 3 / 11 Benign blood vessel neoplasm, Meningeal melanocytoma, Primary melanocytic lesion of meninges
PIK3CA 2 / 11 Capillary malformation, Congenital hemangioma
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 ⇵
GnRH secretion
GNA11, GNAQ, PIK3CA, NRAS, MAP2K2
 KEGG 5 / 65 54.3× 2.34e-8 1.57e-6 ✓ sig.
Hepatocellular carcinoma
PIK3CA, NRAS, TP53, ARID1A, SMARCA4, MAP2K2
 KEGG 6 / 170 24.9× 8.01e-8 4.60e-6 ✓ sig.
Colorectal cancer
PIK3CA, NRAS, MSH6, TP53, MAP2K2
 KEGG 5 / 87 40.6× 1.03e-7 5.72e-6 ✓ sig.
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion
GNA11, GNA14, GNAQ
 Reactome 3 / 8 265× 1.31e-7 7.14e-6 ✓ sig.
Endocrine resistance
PIK3CA, NRAS, TP53, NCOR1, MAP2K2
 KEGG 5 / 99 35.7× 1.97e-7 1.01e-5 ✓ sig.
Acetylcholine regulates insulin secretion
GNA11, GNA14, GNAQ
 Reactome 3 / 9 235× 1.97e-7 1.01e-5 ✓ sig.
Human cytomegalovirus infection
GNA11, GNAQ, PIK3CA, NRAS, TP53, MAP2K2
 KEGG 6 / 226 18.8× 4.32e-7 2.01e-5 ✓ sig.
Sphingolipid signaling pathway
GNAQ, PIK3CA, NRAS, TP53, MAP2K2
 KEGG 5 / 122 29.0× 5.59e-7 2.51e-5 ✓ sig.
Thyroid hormone signaling pathway
PIK3CA, NRAS, TP53, NCOR1, MAP2K2
 KEGG 5 / 122 29.0× 5.59e-7 2.51e-5 ✓ sig.
Growth hormone synthesis, secretion and action
GNA11, GNAQ, PIK3CA, NRAS, MAP2K2
 KEGG 5 / 122 29.0× 5.59e-7 2.51e-5 ✓ sig.
Endometrial cancer
PIK3CA, NRAS, TP53, MAP2K2
 KEGG 4 / 59 47.9× 1.19e-6 4.86e-5 ✓ sig.
Long-term depression
GNA11, GNAQ, NRAS, MAP2K2
 KEGG 4 / 60 47.1× 1.28e-6 5.16e-5 ✓ sig.
Central carbon metabolism in cancer
PIK3CA, NRAS, TP53, MAP2K2
 KEGG 4 / 71 39.8× 2.52e-6 9.18e-5 ✓ sig.
Melanoma
PIK3CA, NRAS, TP53, MAP2K2
 KEGG 4 / 73 38.7× 2.82e-6 1.01e-4 ✓ sig.
Non-small cell lung cancer
PIK3CA, NRAS, TP53, MAP2K2
 KEGG 4 / 73 38.7× 2.82e-6 1.01e-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 ⇵
transcription initiation-coupled chromatin remodeling
TP53, ARID1A, SMARCA4
 GO:0045815 3 / 41 80.4× 6.53e-6 3.91e-4 ✓ sig.
positive regulation of miRNA transcription
WT1, TP53, SMARCA4
 GO:1902895 3 / 56 58.9× 1.68e-5 8.11e-4 ✓ sig.
entrainment of circadian clock
GNA11, GNAQ
 GO:0009649 2 / 8 275× 2.17e-5 9.85e-4 ✓ sig.
phospholipase C-activating dopamine receptor signaling pathway
GNA11, GNA14
 GO:0060158 2 / 8 275× 2.17e-5 9.85e-4 ✓ sig.
phospholipase C-activating serotonin receptor signaling pathway
GNA11, GNAQ
 GO:0007208 2 / 9 244× 2.79e-5 1.18e-3 ✓ sig.
chromatin organization
BAP1, MSH6, ARID1A, SMARCA4, NCOR1
 GO:0006325 5 / 449 12.2× 3.82e-5 1.50e-3 ✓ sig.
phototransduction, visible light
GNA11, GNAQ
 GO:0007603 2 / 13 169× 6.04e-5 2.13e-3 ✓ sig.
G protein-coupled acetylcholine receptor signaling pathway
GNA11, GNAQ
 GO:0007213 2 / 15 147× 8.12e-5 2.65e-3 ✓ sig.
heart development
GNA11, WT1, TP53, MAP2K2
 GO:0007507 4 / 273 16.1× 9.13e-5 2.89e-3 ✓ sig.
negative regulation of androgen receptor signaling pathway
SMARCA4, NCOR1
 GO:0060766 2 / 17 129× 1.05e-4 3.21e-3 ✓ sig.
negative regulation of cell growth
WT1, TP53, SMARCA4
 GO:0030308 3 / 115 28.7× 1.45e-4 4.03e-3 ✓ sig.
nucleosome disassembly
ARID1A, SMARCA4
 GO:0006337 2 / 21 105× 1.62e-4 4.37e-3 ✓ sig.
negative regulation of DNA-templated transcription
WT1, BAP1, TP53, SMARCA4, NCOR1
 GO:0045892 5 / 631 8.7× 1.91e-4 4.92e-3 ✓ sig.
regulation of G0 to G1 transition
ARID1A, SMARCA4
 GO:0070316 2 / 25 87.9× 2.31e-4 5.62e-3 ✓ sig.
regulation of nucleotide-excision repair
ARID1A, SMARCA4
 GO:2000819 2 / 28 78.5× 2.90e-4 6.63e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Meningeal melanocytoma Primary melanocytic lesion of meninges 0.333 3 2.26e-10 2.05e-9 ✓ sig.
Nevus of ota Phakomatosis pigmentovascularis 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Congenital hemangioma Nevus of ota 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Congenital hemangioma Phakomatosis pigmentovascularis 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Anastomosing hemangioma Nevus of ota 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Anastomosing hemangioma Phakomatosis pigmentovascularis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Anastomosing hemangioma Congenital hemangioma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Capillary malformation Congenital hemangioma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Capillary malformation Nevus of ota 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Capillary malformation Phakomatosis pigmentovascularis 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Phakomatosis pigmentovascularis Primary melanocytic lesion of meninges 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Nevus of ota Primary melanocytic lesion of meninges 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Congenital hemangioma Primary melanocytic lesion of meninges 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Anastomosing hemangioma Capillary malformation 0.400 2 7.50e-8 5.34e-7 ✓ sig.
Anastomosing hemangioma Primary melanocytic lesion of meninges 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Capillary malformation Primary melanocytic lesion of meninges 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Meningeal melanocytoma Phakomatosis pigmentovascularis 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Meningeal melanocytoma Nevus of ota 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Congenital hemangioma Meningeal melanocytoma 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Anastomosing hemangioma Meningeal melanocytoma 0.222 2 5.25e-7 3.32e-6 ✓ sig.
Benign blood vessel neoplasm Primary melanocytic lesion of meninges 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Benign blood vessel neoplasm Meningeal melanocytoma 0.167 2 2.62e-6 1.51e-5 ✓ sig.
Hypercalcemia, type ii Hypocalcemia, autosomal dominant 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypocalcemia, autosomal dominant 2 Nevus of ota 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hemangioma Hypocalcemia, autosomal dominant 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hypercalcemia, type ii Nevus of ota 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital hemangioma Hypercalcemia, type ii 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutis marmorata telangiectatica congenita Hypocalcemia, autosomal dominant 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutis marmorata telangiectatica congenita Hypercalcemia, type ii 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutis marmorata telangiectatica congenita Nevus of ota 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Congenital hemangioma Cutis marmorata telangiectatica congenita 0.250 1 2.58e-4 5.38e-4 ✓ sig.