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 191

8 diseases · 16 shared-gene connections
8 Diseases
25 Unique genes
0.225 Avg. similarity score
Patent ductus venosus Most-connected disease (6 links)
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Disease Searched: Ureteral neoplasms 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 ⇵
Patent ductus venosus 6 6 1
Ureteral neoplasms 6 6 1
Urinary bladder calculi 6 6 1
Chronobiology disorder 4 4 4
Congenital nystagmus 3 3 8
Hyperoxia 3 3 3
Pruritus 3 3 13
Atrial and intestinal dysrhythmia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AHR 7 / 8 Chronobiology disorder, Congenital nystagmus, Hyperoxia, Patent ductus venosus and 3 more
SGO1 2 / 8 Atrial and intestinal dysrhythmia, Chronobiology disorder
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 ⇵
Neuroactive ligand-receptor interaction
F2RL1, GRP, HRH1, HRH4, NMB, OPRM1, PDYN, TAC1
 KEGG 8 / 370 10.4× 5.14e-7 2.92e-5 ✓ sig.
Peptide ligand-binding receptors
F2RL1, GRP, NMB, OPRM1, PDYN
 Reactome 5 / 106 22.7× 2.25e-6 1.05e-4 ✓ sig.
Opioid Signalling
OPRM1, PDYN
 Reactome 2 / 3 320× 1.25e-5 4.26e-4 ✓ sig.
G alpha (q) signalling events
F2RL1, GRP, HRH1, NMB, TAC1
 Reactome 5 / 172 14.0× 2.39e-5 7.34e-4 ✓ sig.
Histamine receptors
HRH1, HRH4
 Reactome 2 / 4 240× 2.49e-5 7.57e-4 ✓ sig.
Melanin biosynthesis
OCA2, TYR
 Reactome 2 / 5 192× 4.14e-5 1.15e-3 ✓ sig.
PPARA activates gene expression
AHR, NPAS2, PPARG, CYP1A1
 Reactome 4 / 115 16.7× 8.64e-5 2.06e-3 ✓ sig.
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1)
PAX6, GRP
 Reactome 2 / 14 68.6× 3.73e-4 6.57e-3 ✓ sig.
The canonical retinoid cycle in rods (twilight vision)
MYO7A, RPE65
 Reactome 2 / 20 48.0× 7.72e-4 1.16e-2 ✓ sig.
Lipid and atherosclerosis
PPARG, ATF6, CYP1A1, TNFRSF1A
 KEGG 4 / 216 8.9× 9.57e-4 1.36e-2 ✓ sig.
Xenobiotics
AHR, CYP1A1
 Reactome 2 / 24 40.0× 1.12e-3 1.53e-2 ✓ sig.
G-protein activation
OPRM1, PDYN
 Reactome 2 / 28 34.3× 1.52e-3 1.94e-2 ✓ sig.
Defective ABCB11 causes progressive familial intrahepatic cholestasis 2 and benign recurrent intrahepatic cholestasis 2
ABCB11
 Reactome 1 / 1 480× 2.08e-3 2.44e-2 ✓ sig.
Regulation of commissural axon pathfinding by SLIT and ROBO
ROBO1
 Reactome 1 / 3 160× 6.23e-3 5.25e-2
Biosynthesis of protectins
CYP1A1
 Reactome 1 / 4 120× 8.30e-3 6.28e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
neuropeptide signaling pathway
GRP, NMB, OPRM1, PDYN, TAC1
 GO:0007218 5 / 111 33.7× 3.26e-7 3.37e-5 ✓ sig.
sensory perception
MYO7A, OPRM1, PDYN
 GO:0007600 3 / 16 140× 1.17e-6 9.64e-5 ✓ sig.
visual perception
ATF6, MYO7A, PAX6, RPE65, TYR
 GO:0007601 5 / 215 17.4× 8.48e-6 4.76e-4 ✓ sig.
positive regulation of respiratory gaseous exchange
GRP, NMB
 GO:1903942 2 / 4 374× 1.03e-5 5.52e-4 ✓ sig.
melanin biosynthetic process from tyrosine
OCA2, TYR
 GO:0006583 2 / 4 374× 1.03e-5 5.52e-4 ✓ sig.
positive regulation of lipid metabolic process
PPARG, TNFRSF1A
 GO:0045834 2 / 6 249× 2.57e-5 1.12e-3 ✓ sig.
sensory perception of pain
OPRM1, SCN9A, TAC1
 GO:0019233 3 / 44 51.0× 2.70e-5 1.16e-3 ✓ sig.
inflammatory response
TNFRSF1A, F2RL1, HRH1, HRH4, SCN9A, TAC1
 GO:0006954 6 / 467 9.6× 2.79e-5 1.19e-3 ✓ sig.
positive regulation of cytosolic calcium ion concentration
F2RL1, HRH4, NMB, TAC1
 GO:0007204 4 / 137 21.8× 3.10e-5 1.29e-3 ✓ sig.
positive regulation of behavioral fear response
NPAS2, GRP
 GO:2000987 2 / 7 214× 3.59e-5 1.45e-3 ✓ sig.
adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway
HRH4, OPRM1
 GO:0007197 2 / 8 187× 4.79e-5 1.80e-3 ✓ sig.
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
HRH1, HRH4, OPRM1
 GO:0007187 3 / 54 41.5× 5.02e-5 1.87e-3 ✓ sig.
camera-type eye development
PAX6, RPE65, CYP1A1
 GO:0043010 3 / 74 30.3× 1.29e-4 3.77e-3 ✓ sig.
melanin biosynthetic process
OCA2, TYR
 GO:0042438 2 / 14 107× 1.55e-4 4.32e-3 ✓ sig.
response to toxic substance
AHR, CYP1A1, SCN9A
 GO:0009636 3 / 83 27.0× 1.81e-4 4.87e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Patent ductus venosus Urinary bladder calculi 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Patent ductus venosus Ureteral neoplasms 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Ureteral neoplasms Urinary bladder calculi 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Hyperoxia Urinary bladder calculi 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Hyperoxia Patent ductus venosus 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Hyperoxia Ureteral neoplasms 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Atrial and intestinal dysrhythmia Chronobiology disorder 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Chronobiology disorder Urinary bladder calculi 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Chronobiology disorder Patent ductus venosus 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Chronobiology disorder Ureteral neoplasms 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Congenital nystagmus Patent ductus venosus 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Congenital nystagmus Ureteral neoplasms 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Congenital nystagmus Urinary bladder calculi 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Pruritus Urinary bladder calculi 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Patent ductus venosus Pruritus 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Pruritus Ureteral neoplasms 0.071 1 8.44e-4 1.50e-3 ✓ sig.