Disease Clusters | GeDiPNet

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Cluster 526

5 diseases · 5 shared-gene connections

5 Diseases

9 Unique genes

0.186 Avg. similarity score

Respiratory system neoplasm Most-connected disease (3 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.

Respiratory system neoplasm Wernicke-korsakoff syndrome Acid-base disorder Amed syndrome Blepharitis

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Respiratory system neoplasm	3	3	5
Wernicke-korsakoff syndrome	3	3	2
Acid-base disorder	2	2	2
Amed syndrome	1	1	2
Blepharitis	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
ADH1B	3 / 5	Acid-base disorder, Respiratory system neoplasm, Wernicke-korsakoff syndrome
ALDH2	2 / 5	Amed syndrome, Wernicke-korsakoff syndrome
MC1R	2 / 5	Blepharitis, Respiratory system neoplasm

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 ⇵
Ethanol oxidation ADH5, ALDH2, ADH1B	Reactome	3 / 12	334×	6.38e-8	3.77e-6 ✓ sig.
Fatty acid degradation ADH5, ALDH2, ADH1B	KEGG	3 / 43	93.1×	3.54e-6	1.23e-4 ✓ sig.
Pyruvate metabolism ADH5, ALDH2, ADH1B	KEGG	3 / 47	85.2×	4.64e-6	1.55e-4 ✓ sig.
Glycolysis / Gluconeogenesis ADH5, ALDH2, ADH1B	KEGG	3 / 67	59.8×	1.36e-5	3.76e-4 ✓ sig.
Alcoholic liver disease ADH5, ALDH2, ADH1B	KEGG	3 / 144	27.8×	1.35e-4	2.39e-3 ✓ sig.
Tyrosine metabolism ADH5, ADH1B	KEGG	2 / 36	74.1×	3.10e-4	4.62e-3 ✓ sig.
Retinol metabolism ADH5, ADH1B	KEGG	2 / 68	39.2×	1.11e-3	1.22e-2 ✓ sig.
Drug metabolism - cytochrome P450 ADH5, ADH1B	KEGG	2 / 73	36.6×	1.28e-3	1.37e-2 ✓ sig.
Metabolism of xenobiotics by cytochrome P450 ADH5, ADH1B	KEGG	2 / 79	33.8×	1.49e-3	1.53e-2 ✓ sig.
Metabolism of serotonin ALDH2	Reactome	1 / 2	667×	1.50e-3	1.54e-2 ✓ sig.
Interferon gamma signaling HLA-DQB1, IRF4	Reactome	2 / 87	30.7×	1.81e-3	1.77e-2 ✓ sig.
Th17 cell differentiation HLA-DQB1, IRF4	KEGG	2 / 109	24.5×	2.82e-3	2.44e-2 ✓ sig.
Translocation of ZAP-70 to Immunological synapse HLA-DQB1	Reactome	1 / 19	70.2×	1.42e-2	7.00e-2
Pantothenate and CoA biosynthesis ALDH2	KEGG	1 / 21	63.5×	1.56e-2	7.44e-2
Histidine metabolism ALDH2	KEGG	1 / 22	60.7×	1.64e-2	7.63e-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 ⇵
retinoid metabolic process ADH5, ADH1B	GO:0001523	2 / 38	109×	1.44e-4	4.01e-3 ✓ sig.
nitroglycerin metabolic process ALDH2	GO:0018937	1 / 1	2,076×	4.82e-4	9.24e-3 ✓ sig.
regulation of dopamine biosynthetic process ALDH2	GO:1903179	1 / 1	2,076×	4.82e-4	9.24e-3 ✓ sig.
regulation of serotonin biosynthetic process ALDH2	GO:1905627	1 / 1	2,076×	4.82e-4	9.24e-3 ✓ sig.
ethanol metabolic process ALDH2	GO:0006067	1 / 2	1,038×	9.63e-4	1.42e-2 ✓ sig.
formaldehyde catabolic process ADH5	GO:0046294	1 / 3	692×	1.44e-3	1.79e-2 ✓ sig.
aldehyde catabolic process ALDH2	GO:0046185	1 / 3	692×	1.44e-3	1.79e-2 ✓ sig.
response to nitrosative stress ADH5	GO:0051409	1 / 4	519×	1.93e-3	2.07e-2 ✓ sig.
regulation of T-helper cell differentiation IRF4	GO:0045622	1 / 5	415×	2.41e-3	2.32e-2 ✓ sig.
fatty acid omega-oxidation ADH5	GO:0010430	1 / 6	346×	2.89e-3	2.55e-2 ✓ sig.
cellular detoxification of aldehyde ALDH2	GO:0110095	1 / 7	297×	3.37e-3	2.76e-2 ✓ sig.
positive regulation of feeding behavior MC1R	GO:2000253	1 / 8	260×	3.85e-3	2.94e-2 ✓ sig.
response to redox state ADH5	GO:0051775	1 / 11	189×	5.29e-3	3.43e-2 ✓ sig.
UV-damage excision repair MC1R	GO:0070914	1 / 11	189×	5.29e-3	3.43e-2 ✓ sig.
UV protection MC1R	GO:0009650	1 / 12	173×	5.77e-3	3.56e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Acid-base disorder	Wernicke-korsakoff syndrome	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Amed syndrome	Wernicke-korsakoff syndrome	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Acid-base disorder	Respiratory system neoplasm	0.143	1	6.46e-4	1.09e-3 ✓ sig.
Blepharitis	Respiratory system neoplasm	0.143	1	6.46e-4	1.09e-3 ✓ sig.
Respiratory system neoplasm	Wernicke-korsakoff syndrome	0.143	1	6.46e-4	1.09e-3 ✓ sig.

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