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Cluster 203

8 diseases · 18 shared-gene connections

8 Diseases

18 Unique genes

0.290 Avg. similarity score

Patent ductus venosus Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Patent ductus venosus Ureteral neoplasms Urinary bladder calculi Chronobiology disorder Urinary bladder stone Hyperoxia

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	5	5	4
Urinary bladder stone	5	5	1
Hyperoxia	4	4	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, Hyperoxia, Patent ductus venosus, Pruritus 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	14.4×	2.51e-8	1.97e-6 ✓ sig.
Peptide ligand-binding receptors F2RL1, GRP, NMB, OPRM1, PDYN	Reactome	5 / 106	31.5×	3.81e-7	2.12e-5 ✓ sig.
G alpha (q) signalling events F2RL1, GRP, HRH1, NMB, TAC1	Reactome	5 / 172	19.4×	4.19e-6	1.64e-4 ✓ sig.
Opioid Signalling OPRM1, PDYN	Reactome	2 / 3	445×	6.36e-6	2.29e-4 ✓ sig.
Histamine receptors HRH1, HRH4	Reactome	2 / 4	334×	1.27e-5	4.10e-4 ✓ sig.
PPARA activates gene expression AHR, NPAS2, PPARG, CYP1A1	Reactome	4 / 115	23.2×	2.20e-5	6.46e-4 ✓ sig.
Xenobiotics AHR, CYP1A1	Reactome	2 / 24	55.6×	5.74e-4	8.88e-3 ✓ sig.
G-protein activation OPRM1, PDYN	Reactome	2 / 28	47.7×	7.84e-4	1.13e-2 ✓ sig.
Defective ABCB11 causes progressive familial intrahepatic cholestasis 2 and benign recurrent intrahepatic cholestasis 2 ABCB11	Reactome	1 / 1	667×	1.50e-3	1.85e-2 ✓ sig.
Lipid and atherosclerosis PPARG, CYP1A1, TNFRSF1A	KEGG	3 / 216	9.3×	3.83e-3	3.66e-2 ✓ sig.
G alpha (i) signalling events HRH4, OPRM1, PDYN	Reactome	3 / 249	8.0×	5.71e-3	4.78e-2 ✓ sig.
Biosynthesis of protectins CYP1A1	Reactome	1 / 4	167×	5.98e-3	4.92e-2 ✓ sig.
Tachykinin receptors bind tachykinins TAC1	Reactome	1 / 5	133×	7.47e-3	5.69e-2
TNFR1-mediated ceramide production TNFRSF1A	Reactome	1 / 6	111×	8.96e-3	6.42e-2
Inflammatory mediator regulation of TRP channels F2RL1, HRH1	KEGG	2 / 99	13.5×	9.44e-3	6.63e-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	46.8×	5.44e-8	7.27e-6 ✓ sig.
inflammatory response TNFRSF1A, F2RL1, HRH1, HRH4, SCN9A, TAC1	GO:0006954	6 / 467	13.3×	3.39e-6	2.20e-4 ✓ sig.
positive regulation of respiratory gaseous exchange GRP, NMB	GO:1903942	2 / 4	519×	5.25e-6	3.12e-4 ✓ sig.
positive regulation of cytosolic calcium ion concentration F2RL1, HRH4, NMB, TAC1	GO:0007204	4 / 137	30.3×	7.81e-6	4.30e-4 ✓ sig.
sensory perception of pain OPRM1, SCN9A, TAC1	GO:0019233	3 / 44	70.8×	9.70e-6	5.09e-4 ✓ sig.
positive regulation of lipid metabolic process PPARG, TNFRSF1A	GO:0045834	2 / 6	346×	1.31e-5	6.45e-4 ✓ sig.
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger HRH1, HRH4, OPRM1	GO:0007187	3 / 54	57.7×	1.80e-5	8.28e-4 ✓ sig.
positive regulation of behavioral fear response NPAS2, GRP	GO:2000987	2 / 7	297×	1.84e-5	8.38e-4 ✓ sig.
adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway HRH4, OPRM1	GO:0007197	2 / 8	260×	2.45e-5	1.05e-3 ✓ sig.
response to toxic substance AHR, CYP1A1, SCN9A	GO:0009636	3 / 83	37.5×	6.57e-5	2.21e-3 ✓ sig.
chemical synaptic transmission HRH1, HRH4, PDYN, TAC1	GO:0007268	4 / 236	17.6×	6.60e-5	2.22e-3 ✓ sig.
sensory perception OPRM1, PDYN	GO:0007600	2 / 16	130×	1.04e-4	3.12e-3 ✓ sig.
detection of temperature stimulus involved in sensory perception of pain SCN9A, TAC1	GO:0050965	2 / 20	104×	1.65e-4	4.39e-3 ✓ sig.
xenobiotic metabolic process AHR, CYP1A1, ABCB11	GO:0006805	3 / 120	26.0×	1.96e-4	4.99e-3 ✓ sig.
rhythmic process AHR, NPAS2, PPARG	GO:0048511	3 / 148	21.0×	3.64e-4	7.66e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Patent ductus venosus	Ureteral neoplasms	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Urinary bladder calculi	Urinary bladder stone	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Ureteral neoplasms	Urinary bladder stone	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Ureteral neoplasms	Urinary bladder calculi	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Patent ductus venosus	Urinary bladder stone	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Patent ductus venosus	Urinary bladder calculi	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Hyperoxia	Ureteral neoplasms	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Hyperoxia	Urinary bladder calculi	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Hyperoxia	Urinary bladder stone	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Hyperoxia	Patent ductus venosus	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Atrial and intestinal dysrhythmia	Chronobiology disorder	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Chronobiology disorder	Urinary bladder stone	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Chronobiology disorder	Urinary bladder calculi	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Chronobiology disorder	Ureteral neoplasms	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Chronobiology disorder	Patent ductus venosus	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Patent ductus venosus	Pruritus	0.071	1	8.44e-4	1.48e-3 ✓ sig.
Pruritus	Ureteral neoplasms	0.071	1	8.44e-4	1.48e-3 ✓ sig.
Pruritus	Urinary bladder calculi	0.071	1	8.44e-4	1.48e-3 ✓ sig.

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