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 549

5 diseases · 8 shared-gene connections
5 Diseases
17 Unique genes
0.233 Avg. similarity score
Hidradenoma 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 ⇵
Hidradenoma 4 4 4
Mucoepidermoid carcinoma of submandibular gland 4 4 16
Floor of mouth mucoepidermoid carcinoma 3 3 4
Warthin tumor 3 3 2
Gestational trophoblastic disease 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CRTC1 4 / 5 Floor of mouth mucoepidermoid carcinoma, Hidradenoma, Mucoepidermoid carcinoma of submandibular gland, Warthin tumor
MAML2 4 / 5 Floor of mouth mucoepidermoid carcinoma, Hidradenoma, Mucoepidermoid carcinoma of submandibular gland, Warthin tumor
POU5F1 3 / 5 Gestational trophoblastic disease, Hidradenoma, Mucoepidermoid carcinoma of submandibular gland
EWSR1 2 / 5 Hidradenoma, Mucoepidermoid carcinoma of submandibular gland
HRAS 2 / 5 Floor of mouth mucoepidermoid carcinoma, Mucoepidermoid carcinoma of submandibular gland
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 ⇵
SHC1 events in ERBB4 signaling
ERBB4, HRAS
 Reactome 2 / 14 101× 1.70e-4 2.89e-3 ✓ sig.
GRB2 events in ERBB2 signaling
ERBB4, HRAS
 Reactome 2 / 14 101× 1.70e-4 2.89e-3 ✓ sig.
Human T-cell leukemia virus 1 infection
CRTC1, CRTC3, HRAS, CREB3L2
 KEGG 4 / 224 12.6× 2.32e-4 3.68e-3 ✓ sig.
Signaling by ERBB2 TMD/JMD mutants
ERBB4, HRAS
 Reactome 2 / 22 64.2× 4.28e-4 5.93e-3 ✓ sig.
ATP-dependent chromatin remodeling
BAZ1A, CHD4, ARID1A
 KEGG 3 / 117 18.1× 5.55e-4 7.24e-3 ✓ sig.
Signaling by ERBB2 KD Mutants
ERBB4, HRAS
 Reactome 2 / 25 56.5× 5.55e-4 7.25e-3 ✓ sig.
Circadian Clock
CRTC1, CRTC3
 Reactome 2 / 28 50.5× 6.98e-4 8.62e-3 ✓ sig.
Human papillomavirus infection
MAML2, CHD4, HRAS, CREB3L2
 KEGG 4 / 333 8.5× 1.04e-3 1.17e-2 ✓ sig.
Transcriptional activation of mitochondrial biogenesis
CRTC1, CRTC3
 Reactome 2 / 51 27.7× 2.31e-3 2.12e-2 ✓ sig.
Viral carcinogenesis
CHD4, HRAS, CREB3L2
 KEGG 3 / 205 10.3× 2.79e-3 2.42e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH6
MSH2
 Reactome 1 / 2 353× 2.83e-3 2.44e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH3
MSH2
 Reactome 1 / 2 353× 2.83e-3 2.44e-2 ✓ sig.
Thermogenesis
HRAS, CREB3L2, ARID1A
 KEGG 3 / 234 9.1× 4.06e-3 3.16e-2 ✓ sig.
Defective Mismatch Repair Associated With MSH2
MSH2
 Reactome 1 / 3 235× 4.24e-3 3.26e-2 ✓ sig.
RAS GTPase cycle mutants
HRAS
 Reactome 1 / 3 235× 4.24e-3 3.26e-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 transcription by RNA polymerase II
POU5F1, KMT2D, MAML2, CRTC1, CRTC3, HRAS, CREB3L2
 GO:0045944 7 / 1,208 6.4× 5.07e-5 1.87e-3 ✓ sig.
regulation of cell cycle
HRAS, MSH2, BAP1, BARD1
 GO:0051726 4 / 262 16.8× 7.78e-5 2.57e-3 ✓ sig.
chromatin remodeling
BAZ1A, CHD4, ARID1A, BARD1
 GO:0006338 4 / 320 13.7× 1.68e-4 4.49e-3 ✓ sig.
tissue homeostasis
BAP1, BARD1
 GO:0001894 2 / 27 81.4× 2.70e-4 6.28e-3 ✓ sig.
chromatin organization
KMT2D, CHD4, ARID1A, BAP1
 GO:0006325 4 / 449 9.8× 6.10e-4 1.09e-2 ✓ sig.
cell fate commitment involved in formation of primary germ layer
POU5F1
 GO:0060795 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
beta-catenin-TCF complex assembly
KMT2D
 GO:1904837 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
thrombocyte differentiation
BAP1
 GO:0002574 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
nucleate erythrocyte differentiation
BAP1
 GO:0043363 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
negative regulation of mRNA 3'-end processing
BARD1
 GO:0031441 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
regulation of heterochromatin formation
BAZ1A
 GO:0031445 1 / 1 1,099× 9.10e-4 1.39e-2 ✓ sig.
cellular response to cAMP
CRTC1, CRTC3
 GO:0071320 2 / 58 37.9× 1.25e-3 1.66e-2 ✓ sig.
energy homeostasis
CRTC1, CRTC3
 GO:0097009 2 / 64 34.4× 1.52e-3 1.84e-2 ✓ sig.
protein homotetramerization
CRTC1, CRTC3
 GO:0051289 2 / 66 33.3× 1.61e-3 1.89e-2 ✓ sig.
endodermal-mesodermal cell signaling
POU5F1
 GO:0003133 1 / 2 550× 1.82e-3 2.02e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hidradenoma Mucoepidermoid carcinoma of submandibular gland 0.235 4 7.59e-13 8.22e-12 ✓ sig.
Floor of mouth mucoepidermoid carcinoma Mucoepidermoid carcinoma of submandibular gland 0.167 3 3.62e-9 2.99e-8 ✓ sig.
Floor of mouth mucoepidermoid carcinoma Warthin tumor 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Hidradenoma Warthin tumor 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Floor of mouth mucoepidermoid carcinoma Hidradenoma 0.286 2 3.00e-7 1.96e-6 ✓ sig.
Mucoepidermoid carcinoma of submandibular gland Warthin tumor 0.118 2 1.00e-6 6.10e-6 ✓ sig.
Gestational trophoblastic disease Hidradenoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Gestational trophoblastic disease Mucoepidermoid carcinoma of submandibular gland 0.059 1 1.03e-3 1.57e-3 ✓ sig.