Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 243

7 diseases · 9 shared-gene connections

7 Diseases

10 Unique genes

0.232 Avg. similarity score

Hereditary sensory and motor neuropathy 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.

Hereditary sensory and motor neuropathy Bilateral vestibulopathy Cerebellar ataxia with neuropathy and bilateral vestibular areflexia Cerebellar ataxia, neuropathy, and vestibular areflexia Neuropathy, congenital hypomyelinating Charcot-Marie-Tooth disease type 4

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Hereditary sensory and motor neuropathy	5	5	6
Bilateral vestibulopathy	3	3	1
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia	3	3	1
Cerebellar ataxia, neuropathy, and vestibular areflexia	3	3	2
Neuropathy, congenital hypomyelinating	2	2	5
Charcot-Marie-Tooth disease type 4	1	1	1
RHO-related retinopathy	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
RFC1	4 / 7	Bilateral vestibulopathy, Cerebellar ataxia with neuropathy and bilateral vestibular areflexia, Cerebellar ataxia, neuropathy, and vestibular areflexia, Hereditary sensory and motor neuropathy
EGR2	2 / 7	Hereditary sensory and motor neuropathy, Neuropathy, congenital hypomyelinating
MPZ	2 / 7	Hereditary sensory and motor neuropathy, Neuropathy, congenital hypomyelinating
PRX	2 / 7	Charcot-Marie-Tooth disease type 4, Hereditary sensory and motor neuropathy
RHO	2 / 7	Neuropathy, congenital hypomyelinating, RHO-related retinopathy

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 ⇵
EGR2 and SOX10-mediated initiation of Schwann cell myelination EGR2, MPZ, PMP22, PRX	Reactome	4 / 20	240×	1.17e-9	1.28e-7 ✓ sig.
RUNX1 regulates transcription of genes involved in BCR signaling ELF2	Reactome	1 / 6	200×	4.99e-3	4.37e-2 ✓ sig.
Cell adhesion molecules MPZ, CNTNAP1	KEGG	2 / 160	15.0×	7.40e-3	5.68e-2
Beta-oxidation of pristanoyl-CoA AMACR	Reactome	1 / 9	133×	7.47e-3	5.69e-2
Activation of the phototransduction cascade RHO	Reactome	1 / 9	133×	7.47e-3	5.69e-2
Opsins RHO	Reactome	1 / 10	120×	8.30e-3	6.10e-2
Polymerase switching RFC1	Reactome	1 / 14	85.8×	1.16e-2	7.50e-2
Synthesis of bile acids and bile salts via 24-hydroxycholesterol AMACR	Reactome	1 / 14	85.8×	1.16e-2	7.50e-2
Translesion synthesis by REV1 RFC1	Reactome	1 / 16	75.1×	1.32e-2	8.07e-2
Primary bile acid biosynthesis AMACR	KEGG	1 / 17	70.6×	1.41e-2	8.38e-2
Translesion synthesis by POLK RFC1	Reactome	1 / 17	70.6×	1.41e-2	8.38e-2
Translesion synthesis by POLI RFC1	Reactome	1 / 17	70.6×	1.41e-2	8.38e-2
Polymerase switching on the C-strand of the telomere RFC1	Reactome	1 / 17	70.6×	1.41e-2	8.38e-2
Translesion Synthesis by POLH RFC1	Reactome	1 / 19	63.2×	1.57e-2	8.96e-2
The canonical retinoid cycle in rods (twilight vision) RHO	Reactome	1 / 20	60.1×	1.65e-2	9.23e-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 ⇵
myelination EGR2, MPZ, PMP22, CNTNAP1	GO:0042552	4 / 73	102×	4.42e-8	6.11e-6 ✓ sig.
peripheral nervous system development EGR2, PMP22	GO:0007422	2 / 26	144×	8.32e-5	2.64e-3 ✓ sig.
rhombomere 3 structural organization EGR2	GO:0021659	1 / 1	1,869×	5.35e-4	9.98e-3 ✓ sig.
rhombomere 3 formation EGR2	GO:0021660	1 / 1	1,869×	5.35e-4	9.98e-3 ✓ sig.
rhombomere 5 structural organization EGR2	GO:0021665	1 / 1	1,869×	5.35e-4	9.98e-3 ✓ sig.
rhombomere 5 formation EGR2	GO:0021666	1 / 1	1,869×	5.35e-4	9.98e-3 ✓ sig.
neuromuscular junction development, skeletal muscle fiber CNTNAP1	GO:0098529	1 / 1	1,869×	5.35e-4	9.98e-3 ✓ sig.
rhythmic behavior EGR2	GO:0007622	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
postsynaptic density organization CNTNAP1	GO:0097106	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
paranodal junction maintenance CNTNAP1	GO:1990227	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
rod bipolar cell differentiation RHO	GO:1904389	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
cell aggregation MPZ	GO:0098743	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
thermotaxis RHO	GO:0043052	1 / 2	934×	1.07e-3	1.57e-2 ✓ sig.
positive regulation of Schwann cell differentiation EGR2	GO:0014040	1 / 3	623×	1.60e-3	1.98e-2 ✓ sig.
rhombomere 3 development EGR2	GO:0021569	1 / 3	623×	1.60e-3	1.98e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Hereditary sensory and motor neuropathy	Neuropathy, congenital hypomyelinating	0.200	2	1.26e-6	7.70e-6 ✓ sig.
Bilateral vestibulopathy	Cerebellar ataxia with neuropathy and bilateral vestibular areflexia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Bilateral vestibulopathy	Cerebellar ataxia, neuropathy, and vestibular areflexia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia	Cerebellar ataxia, neuropathy, and vestibular areflexia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Neuropathy, congenital hypomyelinating	RHO-related retinopathy	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Bilateral vestibulopathy	Hereditary sensory and motor neuropathy	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia	Hereditary sensory and motor neuropathy	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Charcot-Marie-Tooth disease type 4	Hereditary sensory and motor neuropathy	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Cerebellar ataxia, neuropathy, and vestibular areflexia	Hereditary sensory and motor neuropathy	0.125	1	7.79e-4	1.39e-3 ✓ sig.

Disease Clusters?