Disease Clusters | GeDiPNet

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Cluster 485

6 diseases · 9 shared-gene connections

6 Diseases

14 Unique genes

0.138 Avg. similarity score

Perrault syndrome Most-connected disease (5 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.

Perrault syndrome Xx gonadal dysgenesis syndrome Childhood-onset sensorineural hearing impairment Hydrops with lactic acidosis and sideroblastic anemia Muscular dystrophy, congenital hearing loss, and ovarian insufficiency syndrome Perrault syndrome 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Perrault syndrome	5	5	14
Xx gonadal dysgenesis syndrome	5	5	8
Childhood-onset sensorineural hearing impairment	2	2	1
Hydrops with lactic acidosis and sideroblastic anemia	2	2	1
Muscular dystrophy, congenital hearing loss, and ovarian insufficiency syndrome	2	2	1
Perrault syndrome 2	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
GGPS1	3 / 6	Muscular dystrophy, congenital hearing loss, and ovarian insufficiency syndrome, Perrault syndrome, Xx gonadal dysgenesis syndrome
HARS2	3 / 6	Perrault syndrome, Perrault syndrome 2, Xx gonadal dysgenesis syndrome
LARS2	3 / 6	Hydrops with lactic acidosis and sideroblastic anemia, Perrault syndrome, Xx gonadal dysgenesis syndrome
PRORP	3 / 6	Childhood-onset sensorineural hearing impairment, Perrault syndrome, Xx gonadal dysgenesis syndrome
ERAL1	2 / 6	Perrault syndrome, Xx gonadal dysgenesis syndrome
HSD17B4	2 / 6	Perrault syndrome, Xx gonadal dysgenesis syndrome
RMND1	2 / 6	Perrault syndrome, Xx gonadal dysgenesis syndrome
TWNK	2 / 6	Perrault syndrome, Xx gonadal dysgenesis 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 ⇵
Mitochondrial tRNA aminoacylation LARS2, HARS2	Reactome	2 / 14	123×	1.14e-4	2.10e-3 ✓ sig.
Mitochondrial translation elongation ERAL1, DAP3, MRPL49	Reactome	3 / 85	30.3×	1.18e-4	2.15e-3 ✓ sig.
Mitochondrial translation termination ERAL1, DAP3, MRPL49	Reactome	3 / 87	29.6×	1.26e-4	2.28e-3 ✓ sig.
Aminoacyl-tRNA biosynthesis LARS2, HARS2	KEGG	2 / 66	26.0×	2.59e-3	2.30e-2 ✓ sig.
rRNA processing in the mitochondrion PRORP	Reactome	1 / 4	214×	4.66e-3	3.48e-2 ✓ sig.
tRNA processing in the mitochondrion PRORP	Reactome	1 / 5	172×	5.82e-3	4.03e-2 ✓ sig.
tRNA modification in the mitochondrion PRORP	Reactome	1 / 6	143×	6.98e-3	4.53e-2 ✓ sig.
Beta-oxidation of pristanoyl-CoA HSD17B4	Reactome	1 / 9	95.3×	1.04e-2	5.84e-2
Beta-oxidation of very long chain fatty acids HSD17B4	Reactome	1 / 11	78.0×	1.28e-2	6.57e-2
alpha-linolenic acid (ALA) metabolism HSD17B4	Reactome	1 / 13	66.0×	1.51e-2	7.27e-2
Primary bile acid biosynthesis HSD17B4	KEGG	1 / 17	50.5×	1.96e-2	8.49e-2
Elastic fibre formation FBN1	Reactome	1 / 18	47.7×	2.08e-2	8.77e-2
Cholesterol biosynthesis GGPS1	Reactome	1 / 21	40.9×	2.42e-2	9.57e-2
Terpenoid backbone biosynthesis GGPS1	KEGG	1 / 23	37.3×	2.65e-2	1.01e-1
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol HSD17B4	Reactome	1 / 24	35.7×	2.76e-2	1.03e-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 ⇵
mitochondrial translation LARS2, HARS2, DAP3, MRPL49	GO:0032543	4 / 93	57.4×	5.54e-7	5.30e-5 ✓ sig.
translation LARS2, HARS2, MRPL49, RMND1	GO:0006412	4 / 310	17.2×	6.52e-5	2.25e-3 ✓ sig.
tRNA aminoacylation for protein translation LARS2, HARS2	GO:0006418	2 / 36	74.2×	3.24e-4	7.08e-3 ✓ sig.
very long-chain fatty-acyl-CoA metabolic process HSD17B4	GO:0036111	1 / 1	1,335×	7.49e-4	1.23e-2 ✓ sig.
geranylgeranyl diphosphate biosynthetic process GGPS1	GO:0033386	1 / 1	1,335×	7.49e-4	1.23e-2 ✓ sig.
activation of protein kinase A activity FBN1	GO:0034199	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
leucyl-tRNA aminoacylation LARS2	GO:0006429	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
histidyl-tRNA aminoacylation HARS2	GO:0006427	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
medium-chain fatty-acyl-CoA metabolic process HSD17B4	GO:0036112	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
geranyl diphosphate biosynthetic process GGPS1	GO:0033384	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
farnesyl diphosphate biosynthetic process GGPS1	GO:0045337	1 / 2	667×	1.50e-3	1.82e-2 ✓ sig.
post-embryonic eye morphogenesis FBN1	GO:0048050	1 / 3	445×	2.25e-3	2.24e-2 ✓ sig.
mitochondrial tRNA 5'-end processing PRORP	GO:0097745	1 / 3	445×	2.25e-3	2.24e-2 ✓ sig.
positive regulation of appetite FBN1	GO:0032100	1 / 4	334×	2.99e-3	2.59e-2 ✓ sig.
sequestering of BMP in extracellular matrix FBN1	GO:0035582	1 / 4	334×	2.99e-3	2.59e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Perrault syndrome	Xx gonadal dysgenesis syndrome	0.533	8	3.66e-26	6.48e-25 ✓ sig.
Childhood-onset sensorineural hearing impairment	Xx gonadal dysgenesis syndrome	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Hydrops with lactic acidosis and sideroblastic anemia	Xx gonadal dysgenesis syndrome	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Muscular dystrophy, congenital hearing loss, and ovarian insufficiency syndrome	Xx gonadal dysgenesis syndrome	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Perrault syndrome 2	Xx gonadal dysgenesis syndrome	0.111	1	5.17e-4	9.13e-4 ✓ sig.
Childhood-onset sensorineural hearing impairment	Perrault syndrome	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Hydrops with lactic acidosis and sideroblastic anemia	Perrault syndrome	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Muscular dystrophy, congenital hearing loss, and ovarian insufficiency syndrome	Perrault syndrome	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Perrault syndrome	Perrault syndrome 2	0.067	1	9.04e-4	1.41e-3 ✓ sig.

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