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Cluster 300

6 diseases · 6 shared-gene connections

6 Diseases

14 Unique genes

0.137 Avg. similarity score

Hyperoxaluria Most-connected disease (4 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.

Hyperoxaluria Pfaundler-hurler syndrome mucopolysaccharidosis type 1 Alanine-glyoxylate aminotransferase deficiency Brachydactyly-elbow wrist dysplasia syndrome primary hyperoxaluria type 3

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Hyperoxaluria	4	4	12
Pfaundler-hurler syndrome	3	3	3
mucopolysaccharidosis type 1	2	2	1
Alanine-glyoxylate aminotransferase deficiency	1	1	1
Brachydactyly-elbow wrist dysplasia syndrome	1	1	2
primary hyperoxaluria type 3	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
IDUA	3 / 6	Hyperoxaluria, mucopolysaccharidosis type 1, Pfaundler-hurler syndrome
AGXT	2 / 6	Alanine-glyoxylate aminotransferase deficiency, Hyperoxaluria
HOGA1	2 / 6	Hyperoxaluria, primary hyperoxaluria type 3
PITX1	2 / 6	Brachydactyly-elbow wrist dysplasia syndrome, Pfaundler-hurler syndrome
SLC26A1	2 / 6	Hyperoxaluria, Pfaundler-hurler syndrome

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 ⇵
Multifunctional anion exchangers SLC26A1, SLC26A6, SLC26A7	Reactome	3 / 9	286×	1.05e-7	6.87e-6 ✓ sig.
Glyoxylate metabolism and glycine degradation AGXT, GRHPR, HOGA1	Reactome	3 / 28	91.9×	4.06e-6	1.60e-4 ✓ sig.
Chagas disease CCL2, CCL5, IL6, NFKB1	KEGG	4 / 103	33.3×	4.78e-6	1.83e-4 ✓ sig.
Glyoxylate and dicarboxylate metabolism AGXT, GRHPR, HOGA1	KEGG	3 / 30	85.8×	5.03e-6	1.91e-4 ✓ sig.
TNF signaling pathway CCL2, CCL5, IL6, NFKB1	KEGG	4 / 119	28.8×	8.50e-6	2.93e-4 ✓ sig.
Interleukin-10 signaling CCL2, CCL5, IL6	Reactome	3 / 47	54.8×	1.98e-5	5.94e-4 ✓ sig.
Influenza A CCL2, CCL5, IL6, NFKB1	KEGG	4 / 173	19.8×	3.72e-5	1.00e-3 ✓ sig.
Herpes simplex virus 1 infection CCL2, CCL5, IL6, NFKB1	KEGG	4 / 182	18.9×	4.54e-5	1.18e-3 ✓ sig.
NOD-like receptor signaling pathway CCL2, CCL5, IL6, NFKB1	KEGG	4 / 187	18.3×	5.04e-5	1.29e-3 ✓ sig.
Lipid and atherosclerosis CCL2, CCL5, IL6, NFKB1	KEGG	4 / 216	15.9×	8.84e-5	2.03e-3 ✓ sig.
Human cytomegalovirus infection CCL2, CCL5, IL6, NFKB1	KEGG	4 / 226	15.2×	1.05e-4	2.35e-3 ✓ sig.
Cytosolic DNA-sensing pathway CCL5, IL6, NFKB1	KEGG	3 / 83	31.0×	1.10e-4	2.42e-3 ✓ sig.
IL-17 signaling pathway CCL2, IL6, NFKB1	KEGG	3 / 94	27.4×	1.59e-4	3.26e-3 ✓ sig.
Rheumatoid arthritis CCL2, CCL5, IL6	KEGG	3 / 95	27.1×	1.64e-4	3.34e-3 ✓ sig.
Viral protein interaction with cytokine and cytokine receptor CCL2, CCL5, IL6	KEGG	3 / 100	25.7×	1.91e-4	3.77e-3 ✓ 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 ⇵
glyoxylate metabolic process AGXT, GRHPR, HOGA1	GO:0046487	3 / 5	801×	3.34e-9	6.52e-7 ✓ sig.
oxalate transport SLC26A1, SLC26A6, SLC26A7	GO:0019532	3 / 11	364×	5.50e-8	7.35e-6 ✓ sig.
sulfate transmembrane transport SLC26A1, SLC26A6, SLC26A7	GO:1902358	3 / 16	250×	1.86e-7	2.04e-5 ✓ sig.
oxalic acid secretion AGXT, SLC26A6	GO:0046724	2 / 2	1,335×	5.21e-7	4.84e-5 ✓ sig.
monocyte chemotaxis CCL2, CCL5, IL6	GO:0002548	3 / 26	154×	8.62e-7	7.34e-5 ✓ sig.
glyoxylate catabolic process AGXT, HOGA1	GO:0009436	2 / 3	890×	1.56e-6	1.18e-4 ✓ sig.
bicarbonate transport SLC26A1, SLC26A6, SLC26A7	GO:0015701	3 / 33	121×	1.80e-6	1.33e-4 ✓ sig.
positive regulation of receptor signaling pathway via STAT CCL5, IL6	GO:1904894	2 / 9	297×	1.87e-5	8.50e-4 ✓ sig.
cellular response to type II interferon CCL2, CCL5, SLC26A6	GO:0071346	3 / 75	53.4×	2.19e-5	9.64e-4 ✓ sig.
chloride transport SLC26A1, SLC26A6, SLC26A7	GO:0006821	3 / 81	49.4×	2.76e-5	1.15e-3 ✓ sig.
cellular response to virus CCL5, IL6, NFKB1	GO:0098586	3 / 89	45.0×	3.66e-5	1.43e-3 ✓ sig.
positive regulation of neuroinflammatory response CCL5, IL6	GO:0150078	2 / 16	167×	6.22e-5	2.12e-3 ✓ sig.
cellular response to tumor necrosis factor CCL2, CCL5, NFKB1	GO:0071356	3 / 107	37.4×	6.35e-5	2.15e-3 ✓ sig.
macrophage chemotaxis CCL2, CCL5	GO:0048246	2 / 17	157×	7.04e-5	2.33e-3 ✓ sig.
chloride transmembrane transport SLC26A1, SLC26A6, SLC26A7	GO:1902476	3 / 114	35.1×	7.66e-5	2.49e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Hyperoxaluria	Pfaundler-hurler syndrome	0.143	2	1.67e-6	9.97e-6 ✓ sig.
mucopolysaccharidosis type 1	Pfaundler-hurler syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Brachydactyly-elbow wrist dysplasia syndrome	Pfaundler-hurler syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Alanine-glyoxylate aminotransferase deficiency	Hyperoxaluria	0.077	1	7.79e-4	1.39e-3 ✓ sig.
Hyperoxaluria	mucopolysaccharidosis type 1	0.077	1	7.79e-4	1.39e-3 ✓ sig.
Hyperoxaluria	primary hyperoxaluria type 3	0.077	1	7.79e-4	1.39e-3 ✓ sig.

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