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 257

8 diseases · 19 shared-gene connections
8 Diseases
12 Unique genes
0.292 Avg. similarity score
Acrodysostosis 1, with or without hormone resistance Most-connected disease (7 links)
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Disease Searched: Primary pigmented nodular adrenocortical disease 1 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 ⇵
Acrodysostosis 1, with or without hormone resistance 7 7 1
Atrial myxoma 7 7 1
Primary pigmented nodular adrenocortical disease 1 7 7 1
Acrodysostosis 4 4 2
Melanotic neurilemmoma 4 4 2
Oncocytic neoplasm 3 3 4
Peripheral nerve schwannoma 3 3 4
Testicular large cell calcifying sertoli cell tumor 3 3 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
PRKAR1A 8 / 8 Acrodysostosis, Acrodysostosis 1, with or without hormone resistance, Atrial myxoma, Melanotic neurilemmoma and 4 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 ⇵
DARPP-32 events
PDE4D, PRKAR1A
 Reactome 2 / 19 105× 1.55e-4 2.68e-3 ✓ sig.
RHO GTPases activate PAKs
FLNA, NF2
 Reactome 2 / 23 87.0× 2.29e-4 3.65e-3 ✓ sig.
Hippo signaling pathway - multiple species
NF2, LATS2
 KEGG 2 / 29 69.0× 3.66e-4 5.24e-3 ✓ sig.
Hippo signaling pathway
CTNNB1, NF2, LATS2
 KEGG 3 / 157 19.1× 4.42e-4 6.06e-3 ✓ sig.
Proteoglycans in cancer
CTNNB1, FLNA, CBL
 KEGG 3 / 204 14.7× 9.49e-4 1.09e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH6
MSH2
 Reactome 1 / 2 500× 2.00e-3 1.90e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH3
MSH2
 Reactome 1 / 2 500× 2.00e-3 1.90e-2 ✓ sig.
Bacterial invasion of epithelial cells
CTNNB1, CBL
 KEGG 2 / 78 25.7× 2.63e-3 2.33e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH2
MSH2
 Reactome 1 / 3 334× 2.99e-3 2.54e-2 ✓ sig.
Colorectal cancer
CTNNB1, MSH2
 KEGG 2 / 87 23.0× 3.27e-3 2.71e-2 ✓ sig.
LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production
CTNNB1
 Reactome 1 / 5 200× 4.99e-3 3.64e-2 ✓ sig.
InlB-mediated entry of Listeria monocytogenes into host cell
CBL
 Reactome 1 / 7 143× 6.97e-3 4.53e-2 ✓ sig.
CREB1 phosphorylation through the activation of Adenylate Cyclase
PRKAR1A
 Reactome 1 / 7 143× 6.97e-3 4.53e-2 ✓ sig.
Binding of TCF/LEF:CTNNB1 to target gene promoters
CTNNB1
 Reactome 1 / 8 125× 7.97e-3 4.94e-2 ✓ sig.
RUNX3 regulates WNT signaling
CTNNB1
 Reactome 1 / 8 125× 7.97e-3 4.94e-2 ✓ 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 ⇵
positive regulation of cell differentiation
CTNNB1, SMARCB1, NF2
 GO:0045597 3 / 83 56.3× 1.81e-5 8.57e-4 ✓ sig.
ectoderm development
CTNNB1, NF2
 GO:0007398 2 / 15 208× 3.95e-5 1.54e-3 ✓ sig.
positive regulation of neural precursor cell proliferation
CTNNB1, FLNA
 GO:2000179 2 / 21 148× 7.88e-5 2.60e-3 ✓ sig.
negative regulation of cAMP/PKA signal transduction
PDE4D, PRKAR1A
 GO:0141162 2 / 28 111× 1.42e-4 3.97e-3 ✓ sig.
protein localization to cell surface
CTNNB1, FLNA
 GO:0034394 2 / 32 97.3× 1.86e-4 4.82e-3 ✓ sig.
mesoderm formation
PRKAR1A, NF2
 GO:0001707 2 / 38 82.0× 2.62e-4 6.17e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
KMT2A, SMARCB1
 GO:0045815 2 / 41 76.0× 3.06e-4 6.87e-3 ✓ sig.
regulation of neurogenesis
CTNNB1, NF2
 GO:0050767 2 / 49 63.6× 4.37e-4 8.67e-3 ✓ sig.
thymus development
CTNNB1, ASXL1
 GO:0048538 2 / 50 62.3× 4.55e-4 8.92e-3 ✓ sig.
odontogenesis of dentin-containing tooth
CTNNB1, NF2
 GO:0042475 2 / 56 55.6× 5.71e-4 1.04e-2 ✓ sig.
glial cell fate determination
CTNNB1
 GO:0007403 1 / 1 1,557× 6.42e-4 1.11e-2 ✓ sig.
canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation
CTNNB1
 GO:0044338 1 / 1 1,557× 6.42e-4 1.11e-2 ✓ sig.
lung cell differentiation
CTNNB1
 GO:0060479 1 / 1 1,557× 6.42e-4 1.11e-2 ✓ sig.
cranial ganglion development
CTNNB1
 GO:0061550 1 / 1 1,557× 6.42e-4 1.11e-2 ✓ sig.
regulation of membrane repolarization during atrial cardiac muscle cell action potential
FLNA
 GO:1905000 1 / 1 1,557× 6.42e-4 1.11e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Acrodysostosis 1, with or without hormone resistance Atrial myxoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acrodysostosis 1, with or without hormone resistance Primary pigmented nodular adrenocortical disease 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atrial myxoma Primary pigmented nodular adrenocortical disease 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acrodysostosis Acrodysostosis 1, with or without hormone resistance 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrodysostosis Primary pigmented nodular adrenocortical disease 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrodysostosis 1, with or without hormone resistance Melanotic neurilemmoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrodysostosis Atrial myxoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atrial myxoma Melanotic neurilemmoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanotic neurilemmoma Primary pigmented nodular adrenocortical disease 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acrodysostosis Melanotic neurilemmoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Primary pigmented nodular adrenocortical disease 1 Testicular large cell calcifying sertoli cell tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Acrodysostosis 1, with or without hormone resistance Testicular large cell calcifying sertoli cell tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Atrial myxoma Testicular large cell calcifying sertoli cell tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Peripheral nerve schwannoma Primary pigmented nodular adrenocortical disease 1 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Acrodysostosis 1, with or without hormone resistance Peripheral nerve schwannoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Atrial myxoma Peripheral nerve schwannoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Oncocytic neoplasm Primary pigmented nodular adrenocortical disease 1 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Atrial myxoma Oncocytic neoplasm 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Acrodysostosis 1, with or without hormone resistance Oncocytic neoplasm 0.200 1 2.58e-4 5.38e-4 ✓ sig.