Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 517

5 diseases · 9 shared-gene connections

5 Diseases

4 Unique genes

0.343 Avg. similarity score

Cowchock syndrome 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.

Cowchock syndrome Severe x-linked mitochondrial encephalomyopathy X-linked hereditary sensory and autonomic neuropathy with deafness Beta-hydroxyisobutyryl-coa deacylase deficiency X-linked spondyloepimetaphyseal dysplasia

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cowchock syndrome	4	4	2
Severe x-linked mitochondrial encephalomyopathy	4	4	1
X-linked hereditary sensory and autonomic neuropathy with deafness	4	4	1
Beta-hydroxyisobutyryl-coa deacylase deficiency	3	3	3
X-linked spondyloepimetaphyseal dysplasia	3	3	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
AIFM1	5 / 5	Beta-hydroxyisobutyryl-coa deacylase deficiency, Cowchock syndrome, Severe x-linked mitochondrial encephalomyopathy, X-linked hereditary sensory and autonomic neuropathy with deafness and 1 more
RAB33A	2 / 5	Beta-hydroxyisobutyryl-coa deacylase deficiency, Cowchock 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 ⇵
Defective CHST3 causes SEDCJD BGN	Reactome	1 / 8	375×	2.66e-3	2.34e-2 ✓ sig.
Defective CHST14 causes EDS, musculocontractural type BGN	Reactome	1 / 8	375×	2.66e-3	2.34e-2 ✓ sig.
Defective CHSY1 causes TPBS BGN	Reactome	1 / 8	375×	2.66e-3	2.34e-2 ✓ sig.
Dermatan sulfate biosynthesis BGN	Reactome	1 / 11	273×	3.66e-3	2.93e-2 ✓ sig.
CS/DS degradation BGN	Reactome	1 / 14	214×	4.66e-3	3.48e-2 ✓ sig.
Defective B4GALT7 causes EDS, progeroid type BGN	Reactome	1 / 20	150×	6.65e-3	4.39e-2 ✓ sig.
Defective B3GAT3 causes JDSSDHD BGN	Reactome	1 / 20	150×	6.65e-3	4.39e-2 ✓ sig.
Defective B3GALT6 causes EDSP2 and SEMDJL1 BGN	Reactome	1 / 20	150×	6.65e-3	4.39e-2 ✓ sig.
Branched-chain amino acid catabolism HIBCH	Reactome	1 / 20	150×	6.65e-3	4.39e-2 ✓ sig.
Chondroitin sulfate biosynthesis BGN	Reactome	1 / 20	150×	6.65e-3	4.39e-2 ✓ sig.
A tetrasaccharide linker sequence is required for GAG synthesis BGN	Reactome	1 / 26	115×	8.63e-3	5.19e-2
beta-Alanine metabolism HIBCH	KEGG	1 / 31	96.9×	1.03e-2	5.79e-2
Propanoate metabolism HIBCH	KEGG	1 / 32	93.8×	1.06e-2	5.90e-2
TBC/RABGAPs RAB33A	Reactome	1 / 46	65.3×	1.52e-2	7.32e-2
Valine, leucine and isoleucine degradation HIBCH	KEGG	1 / 48	62.6×	1.59e-2	7.51e-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 ⇵
protein import into mitochondrial intermembrane space AIFM1	GO:0045041	1 / 3	1,557×	6.42e-4	1.11e-2 ✓ sig.
mitochondrial disulfide relay system AIFM1	GO:0160203	1 / 3	1,557×	6.42e-4	1.11e-2 ✓ sig.
L-valine catabolic process HIBCH	GO:0006574	1 / 5	934×	1.07e-3	1.51e-2 ✓ sig.
mitochondrial respiratory chain complex assembly AIFM1	GO:0033108	1 / 6	779×	1.28e-3	1.67e-2 ✓ sig.
articular cartilage development BGN	GO:0061975	1 / 6	779×	1.28e-3	1.67e-2 ✓ sig.
cellular response to aldosterone AIFM1	GO:1904045	1 / 7	667×	1.50e-3	1.82e-2 ✓ sig.
positive regulation of necroptotic process AIFM1	GO:0060545	1 / 8	584×	1.71e-3	1.96e-2 ✓ sig.
response to L-glutamate AIFM1	GO:1902065	1 / 12	389×	2.57e-3	2.40e-2 ✓ sig.
positive regulation of programmed cell death AIFM1	GO:0043068	1 / 17	275×	3.63e-3	2.86e-2 ✓ sig.
Rab protein signal transduction RAB33A	GO:0032482	1 / 17	275×	3.63e-3	2.86e-2 ✓ sig.
cellular response to nitric oxide AIFM1	GO:0071732	1 / 17	275×	3.63e-3	2.86e-2 ✓ sig.
branched-chain amino acid catabolic process HIBCH	GO:0009083	1 / 18	260×	3.85e-3	2.94e-2 ✓ sig.
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress AIFM1	GO:0070059	1 / 36	130×	7.68e-3	4.09e-2 ✓ sig.
cellular response to estradiol stimulus AIFM1	GO:0071392	1 / 36	130×	7.68e-3	4.09e-2 ✓ sig.
blood vessel remodeling BGN	GO:0001974	1 / 42	111×	8.96e-3	4.41e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Beta-hydroxyisobutyryl-coa deacylase deficiency	Cowchock syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Severe x-linked mitochondrial encephalomyopathy	X-linked hereditary sensory and autonomic neuropathy with deafness	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cowchock syndrome	X-linked hereditary sensory and autonomic neuropathy with deafness	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cowchock syndrome	Severe x-linked mitochondrial encephalomyopathy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Severe x-linked mitochondrial encephalomyopathy	X-linked spondyloepimetaphyseal dysplasia	0.333	1	1.29e-4	3.27e-4 ✓ sig.
X-linked hereditary sensory and autonomic neuropathy with deafness	X-linked spondyloepimetaphyseal dysplasia	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Beta-hydroxyisobutyryl-coa deacylase deficiency	X-linked hereditary sensory and autonomic neuropathy with deafness	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Beta-hydroxyisobutyryl-coa deacylase deficiency	Severe x-linked mitochondrial encephalomyopathy	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cowchock syndrome	X-linked spondyloepimetaphyseal dysplasia	0.250	1	2.58e-4	5.38e-4 ✓ sig.

Disease Clusters?