Disease Clusters | GeDiPNet

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Cluster 242

7 diseases · 10 shared-gene connections

7 Diseases

29 Unique genes

0.139 Avg. similarity score

Canavan disease Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Canavan 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.

Canavan disease Genetic infertility Infertility Fraser syndrome Olmsted syndrome primary ciliary dyskinesia 20

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Canavan disease	4	4	2
Genetic infertility	4	4	1
Infertility	4	4	8
Fraser syndrome	3	3	20
Olmsted syndrome	3	3	3
primary ciliary dyskinesia 20	1	1	1
spermatogenic failure 5	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SPATA22	5 / 7	Canavan disease, Fraser syndrome, Genetic infertility, Infertility and 1 more
ASPA	2 / 7	Canavan disease, Fraser syndrome
AURKC	2 / 7	Infertility, spermatogenic failure 5
ODAD1	2 / 7	Fraser syndrome, primary ciliary dyskinesia 20

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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
FGFR1c and Klotho ligand binding and activation KL	Reactome	1 / 3	138×	7.23e-3	5.77e-2
Ligand-receptor interactions PTCH1	Reactome	1 / 7	59.2×	1.68e-2	9.68e-2
ECM-receptor interaction FRAS1, FREM2	KEGG	2 / 89	9.3×	1.94e-2	1.05e-1
Longevity regulating pathway EHMT2, KL	KEGG	2 / 90	9.2×	1.98e-2	1.06e-1
Prostanoid ligand receptors PTGER2	Reactome	1 / 9	46.0×	2.15e-2	1.12e-1
Inflammatory mediator regulation of TRP channels PTGER2, TRPV3	KEGG	2 / 99	8.4×	2.36e-2	1.18e-1
SLBP independent Processing of Histone Pre-mRNAs LSM10	Reactome	1 / 10	41.4×	2.39e-2	1.18e-1
SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs LSM10	Reactome	1 / 11	37.6×	2.63e-2	1.25e-1
Aspartate and asparagine metabolism ASPA	Reactome	1 / 12	34.5×	2.86e-2	1.31e-1
TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain PERP	Reactome	1 / 14	29.6×	3.33e-2	1.42e-1
ADORA2B mediated anti-inflammatory cytokines production GNB5, PTGER2	Reactome	2 / 128	6.5×	3.79e-2	1.52e-1
Phospholipase C-mediated cascade: FGFR1 KL	Reactome	1 / 16	25.9×	3.80e-2	1.52e-1
Trafficking of GluR2-containing AMPA receptors GRIP1	Reactome	1 / 17	24.4×	4.03e-2	1.57e-1
G beta:gamma signalling through BTK GNB5	Reactome	1 / 18	23.0×	4.26e-2	1.62e-1
Activation of SMO PTCH1	Reactome	1 / 18	23.0×	4.26e-2	1.62e-1

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

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
mammary gland duct morphogenesis PTCH1, PERP	GO:0060603	2 / 8	161×	6.47e-5	2.26e-3 ✓ sig.
negative regulation of gene expression via chromosomal CpG island methylation WT1, EHMT2	GO:0044027	2 / 16	80.5×	2.75e-4	6.53e-3 ✓ sig.
energy reserve metabolic process KL, LEPR	GO:0006112	2 / 16	80.5×	2.75e-4	6.53e-3 ✓ sig.
spermatid development PTCH1, EHMT2, SYCP3	GO:0007286	3 / 120	16.1×	8.35e-4	1.39e-2 ✓ sig.
meiotic cell cycle SPATA22, AURKC, SYCP3	GO:0051321	3 / 137	14.1×	1.23e-3	1.77e-2 ✓ sig.
negative regulation of metanephric glomerular mesangial cell proliferation WT1	GO:0072302	1 / 1	644×	1.55e-3	2.03e-2 ✓ sig.
acetate metabolic process ASPA	GO:0006083	1 / 1	644×	1.55e-3	2.03e-2 ✓ sig.
negative regulation of hair cycle TRPV3	GO:0042636	1 / 1	644×	1.55e-3	2.03e-2 ✓ sig.
branching involved in ureteric bud morphogenesis PTCH1, WT1	GO:0001658	2 / 45	28.6×	2.21e-3	2.48e-2 ✓ sig.
morphogenesis of an epithelium FRAS1, FREM2	GO:0002009	2 / 51	25.3×	2.83e-3	2.84e-2 ✓ sig.
regulation of animal organ formation WT1	GO:0003156	1 / 2	322×	3.10e-3	2.98e-2 ✓ sig.
adrenal cortex formation WT1	GO:0035802	1 / 2	322×	3.10e-3	2.98e-2 ✓ sig.
visceral serous pericardium development WT1	GO:0061032	1 / 2	322×	3.10e-3	2.98e-2 ✓ sig.
nephron tubule morphogenesis WT1	GO:0072078	1 / 2	322×	3.10e-3	2.98e-2 ✓ sig.
posterior mesonephric tubule development WT1	GO:0072166	1 / 2	322×	3.10e-3	2.98e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Canavan disease	Fraser syndrome	0.095	2	1.60e-6	9.10e-6 ✓ sig.
Canavan disease	Genetic infertility	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Genetic infertility	Olmsted syndrome	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Canavan disease	Olmsted syndrome	0.200	1	3.90e-4	8.67e-4 ✓ sig.
Genetic infertility	Infertility	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Infertility	spermatogenic failure 5	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Canavan disease	Infertility	0.100	1	1.04e-3	1.74e-3 ✓ sig.
Fraser syndrome	Genetic infertility	0.048	1	1.30e-3	2.06e-3 ✓ sig.
Fraser syndrome	primary ciliary dyskinesia 20	0.048	1	1.30e-3	2.06e-3 ✓ sig.
Infertility	Olmsted syndrome	0.091	1	1.56e-3	2.38e-3 ✓ sig.

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