Disease Clusters | GeDiPNet

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Cluster 120

12 diseases · 31 shared-gene connections

12 Diseases

12 Unique genes

0.378 Avg. similarity score

Clouston syndrome Most-connected disease (9 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Palmoplantar hyperkeratosis 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.

Palmoplantar hyperkeratosis Clouston syndrome Senter syndrome Ectodermal dysplasia, hidrotic, autosomal dominant Keratitis-ichthyosis-deafness syndrome Deafness, autosomal dominant, 3b

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Clouston syndrome	9	9	2
Senter syndrome	9	9	2
Ectodermal dysplasia, hidrotic, autosomal dominant	6	6	1
Keratitis-ichthyosis-deafness syndrome	6	6	3
Deafness, autosomal dominant, 3b	5	5	1
Deafness, autosomal recessive 1b	5	5	1
Deafness, x-linked	5	5	10
Hearing loss with stapes fixation	5	5	3
Palmoplantar hyperkeratosis	5	5	2
X-linked hearing loss with perilymphatic gusher	5	5	3
Ichthyosiform erythroderma, corneal involvement, and hearing loss	1	1	1
X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
GJB6	10 / 12	Clouston syndrome, Deafness, autosomal dominant, 3b, Deafness, autosomal recessive 1b, Deafness, x-linked and 6 more
GJB2	6 / 12	Clouston syndrome, Deafness, x-linked, Hearing loss with stapes fixation, Keratitis-ichthyosis-deafness syndrome and 2 more
POU3F4	3 / 12	Deafness, x-linked, Hearing loss with stapes fixation, X-linked hearing loss with perilymphatic gusher
AP1B1	2 / 12	Ichthyosiform erythroderma, corneal involvement, and hearing loss, Keratitis-ichthyosis-deafness syndrome
GPRASP2	2 / 12	Deafness, x-linked, X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism 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 ⇵
Transport of connexons to the plasma membrane GJB2	Reactome	1 / 1	1,001×	9.99e-4	1.13e-2 ✓ sig.
5-Phosphoribose 1-diphosphate biosynthesis PRPS1	Reactome	1 / 3	334×	2.99e-3	2.54e-2 ✓ sig.
Nef mediated downregulation of MHC class I complex cell surface expression AP1B1	Reactome	1 / 10	100×	9.95e-3	5.67e-2
Dissolution of Fibrin Clot SERPINB8	Reactome	1 / 13	77.0×	1.29e-2	6.62e-2
Extracellular matrix organization COL4A6	Reactome	1 / 15	66.7×	1.49e-2	7.22e-2
Anchoring fibril formation COL4A6	Reactome	1 / 15	66.7×	1.49e-2	7.22e-2
Gap junction assembly GJB6	Reactome	1 / 18	55.6×	1.78e-2	8.03e-2
Crosslinking of collagen fibrils COL4A6	Reactome	1 / 18	55.6×	1.78e-2	8.03e-2
Non-integrin membrane-ECM interactions COL4A6	Reactome	1 / 24	41.7×	2.37e-2	9.46e-2
Laminin interactions COL4A6	Reactome	1 / 28	35.7×	2.76e-2	1.03e-1
Pentose phosphate pathway PRPS1	KEGG	1 / 31	32.3×	3.06e-2	1.10e-1
Lysosome Vesicle Biogenesis AP1B1	Reactome	1 / 35	28.6×	3.44e-2	1.17e-1
Collagen chain trimerization COL4A6	Reactome	1 / 44	22.7×	4.31e-2	1.33e-1
TBC/RABGAPs RAB33A	Reactome	1 / 46	21.8×	4.50e-2	1.36e-1
Assembly of collagen fibrils and other multimeric structures COL4A6	Reactome	1 / 51	19.6×	4.98e-2	1.44e-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 ⇵
gap junction-mediated intercellular transport GJB2, GJB6	GO:1990349	2 / 6	519×	5.66e-6	3.49e-4 ✓ sig.
cell communication by electrical coupling GJB2, GJB6	GO:0010644	2 / 7	445×	7.92e-6	4.55e-4 ✓ sig.
gap junction assembly GJB2, GJB6	GO:0016264	2 / 8	389×	1.06e-5	5.67e-4 ✓ sig.
sensory perception of sound GJB2, GJB6, POU3F4	GO:0007605	3 / 162	28.8×	1.33e-4	3.79e-3 ✓ sig.
hematopoietic stem cell homeostasis ARMCX5-GPRASP2, GPRASP2	GO:0061484	2 / 30	104×	1.63e-4	4.38e-3 ✓ sig.
cell communication GJB2, GJB6	GO:0007154	2 / 80	38.9×	1.16e-3	1.59e-2 ✓ sig.
urate biosynthetic process PRPS1	GO:0034418	1 / 2	779×	1.28e-3	1.67e-2 ✓ sig.
hypoxanthine biosynthetic process PRPS1	GO:0046101	1 / 2	779×	1.28e-3	1.67e-2 ✓ sig.
protein import into mitochondrial intermembrane space AIFM1	GO:0045041	1 / 3	519×	1.93e-3	2.07e-2 ✓ sig.
mitochondrial disulfide relay system AIFM1	GO:0160203	1 / 3	519×	1.93e-3	2.07e-2 ✓ sig.
ribonucleoside monophosphate biosynthetic process PRPS1	GO:0009156	1 / 4	389×	2.57e-3	2.40e-2 ✓ sig.
basolateral protein secretion AP1B1	GO:0110010	1 / 5	311×	3.21e-3	2.69e-2 ✓ sig.
ear morphogenesis GJB6	GO:0042471	1 / 5	311×	3.21e-3	2.69e-2 ✓ sig.
5-phosphoribose 1-diphosphate biosynthetic process PRPS1	GO:0006015	1 / 5	311×	3.21e-3	2.69e-2 ✓ sig.
negative regulation of mesenchymal cell apoptotic process POU3F4	GO:2001054	1 / 6	260×	3.85e-3	2.94e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Hearing loss with stapes fixation	X-linked hearing loss with perilymphatic gusher	0.750	3	1.62e-12	1.71e-11 ✓ sig.
Deafness, x-linked	X-linked hearing loss with perilymphatic gusher	0.273	3	1.94e-10	1.78e-9 ✓ sig.
Deafness, x-linked	Hearing loss with stapes fixation	0.273	3	1.94e-10	1.78e-9 ✓ sig.
Clouston syndrome	Senter syndrome	0.667	2	8.34e-9	6.60e-8 ✓ sig.
Clouston syndrome	Keratitis-ichthyosis-deafness syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Senter syndrome	X-linked hearing loss with perilymphatic gusher	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Keratitis-ichthyosis-deafness syndrome	Senter syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Hearing loss with stapes fixation	Senter syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Clouston syndrome	Hearing loss with stapes fixation	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Clouston syndrome	X-linked hearing loss with perilymphatic gusher	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Keratitis-ichthyosis-deafness syndrome	X-linked hearing loss with perilymphatic gusher	0.400	2	7.50e-8	5.34e-7 ✓ sig.
Hearing loss with stapes fixation	Keratitis-ichthyosis-deafness syndrome	0.400	2	7.50e-8	5.34e-7 ✓ sig.
Clouston syndrome	Deafness, x-linked	0.182	2	3.75e-7	2.42e-6 ✓ sig.
Deafness, x-linked	Senter syndrome	0.182	2	3.75e-7	2.42e-6 ✓ sig.
Deafness, autosomal recessive 1b	Ectodermal dysplasia, hidrotic, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Deafness, autosomal dominant, 3b	Deafness, autosomal recessive 1b	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Deafness, autosomal dominant, 3b	Ectodermal dysplasia, hidrotic, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Deafness, autosomal dominant, 3b	Palmoplantar hyperkeratosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Clouston syndrome	Ectodermal dysplasia, hidrotic, autosomal dominant	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Ectodermal dysplasia, hidrotic, autosomal dominant	Palmoplantar hyperkeratosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Ectodermal dysplasia, hidrotic, autosomal dominant	Senter syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Clouston syndrome	Deafness, autosomal dominant, 3b	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Deafness, autosomal recessive 1b	Palmoplantar hyperkeratosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Deafness, autosomal recessive 1b	Senter syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Clouston syndrome	Deafness, autosomal recessive 1b	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Deafness, autosomal dominant, 3b	Senter syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Ichthyosiform erythroderma, corneal involvement, and hearing loss	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Ectodermal dysplasia, hidrotic, autosomal dominant	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Clouston syndrome	Palmoplantar hyperkeratosis	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Palmoplantar hyperkeratosis	Senter syndrome	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Deafness, x-linked	X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome	0.091	1	6.46e-4	1.09e-3 ✓ sig.

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