Disease Clusters | GeDiPNet

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Cluster 68

14 diseases · 34 shared-gene connections

14 Diseases

16 Unique genes

0.303 Avg. similarity score

Senter syndrome Most-connected disease (10 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.

Senter syndrome Keratitis-ichthyosis-deafness syndrome Bart-pumphrey syndrome Deafness, digenic Keratitis ichthyosis hearing loss syndrome Clouston syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Senter syndrome	10	10	2
Keratitis-ichthyosis-deafness syndrome	8	8	3
Bart-pumphrey syndrome	6	6	1
Deafness, digenic	6	6	2
Keratitis ichthyosis hearing loss syndrome	6	6	1
Clouston syndrome	5	5	1
Deafness, x-linked	5	5	10
Hearing loss with stapes fixation	5	5	3
Vohwinkel syndrome	5	5	2
X-linked hearing loss with perilymphatic gusher	5	5	3
Xeroderma	4	4	4
Peripheral neuropathy with sensorineural hearing impairment syndrome	1	1	1
X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome	1	1	1
ichthyosiform erythroderma, corneal involvement, and hearing loss	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
GJB2	10 / 14	Bart-pumphrey syndrome, Deafness, digenic, Deafness, x-linked, Hearing loss with stapes fixation and 6 more
GJB6	6 / 14	Clouston syndrome, Deafness, x-linked, Hearing loss with stapes fixation, Keratitis-ichthyosis-deafness syndrome and 2 more
POU3F4	3 / 14	Deafness, x-linked, Hearing loss with stapes fixation, X-linked hearing loss with perilymphatic gusher
AP1B1	2 / 14	ichthyosiform erythroderma, corneal involvement, and hearing loss, Keratitis-ichthyosis-deafness syndrome
GJB3	2 / 14	Deafness, digenic, Peripheral neuropathy with sensorineural hearing impairment syndrome
GPRASP2	2 / 14	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 ⇵
Gap junction assembly GJB6, GJB3	Reactome	2 / 18	83.4×	2.51e-4	4.67e-3 ✓ sig.
Transport of connexons to the plasma membrane GJB2	Reactome	1 / 1	751×	1.33e-3	1.68e-2 ✓ sig.
5-Phosphoribose 1-diphosphate biosynthesis PRPS1	Reactome	1 / 3	250×	3.99e-3	3.77e-2 ✓ sig.
Formation of the cornified envelope LORICRIN, KRT2	Reactome	2 / 130	11.5×	1.26e-2	7.86e-2
Nef mediated downregulation of MHC class I complex cell surface expression AP1B1	Reactome	1 / 10	75.1×	1.32e-2	8.07e-2
Extracellular matrix organization COL4A6	Reactome	1 / 15	50.0×	1.98e-2	1.02e-1
Anchoring fibril formation COL4A6	Reactome	1 / 15	50.0×	1.98e-2	1.02e-1
Crosslinking of collagen fibrils COL4A6	Reactome	1 / 18	41.7×	2.37e-2	1.13e-1
Non-integrin membrane-ECM interactions COL4A6	Reactome	1 / 24	31.3×	3.15e-2	1.32e-1
Laminin interactions COL4A6	Reactome	1 / 28	26.8×	3.67e-2	1.44e-1
Pentose phosphate pathway PRPS1	KEGG	1 / 31	24.2×	4.05e-2	1.53e-1
Lysosome Vesicle Biogenesis AP1B1	Reactome	1 / 35	21.4×	4.57e-2	1.63e-1
Collagen chain trimerization COL4A6	Reactome	1 / 44	17.1×	5.71e-2	1.84e-1
TBC/RABGAPs RAB33A	Reactome	1 / 46	16.3×	5.96e-2	1.88e-1
Assembly of collagen fibrils and other multimeric structures COL4A6	Reactome	1 / 51	14.7×	6.59e-2	1.98e-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	389×	1.03e-5	5.33e-4 ✓ sig.
cell communication by electrical coupling GJB2, GJB6	GO:0010644	2 / 7	334×	1.44e-5	6.94e-4 ✓ sig.
gap junction assembly GJB2, GJB6	GO:0016264	2 / 8	292×	1.92e-5	8.69e-4 ✓ sig.
cell communication GJB2, GJB6, GJB3	GO:0007154	3 / 80	43.8×	4.06e-5	1.54e-3 ✓ sig.
peptide cross-linking LORICRIN, KRT2	GO:0018149	2 / 19	123×	1.17e-4	3.40e-3 ✓ sig.
hematopoietic stem cell homeostasis ARMCX5-GPRASP2, GPRASP2	GO:0061484	2 / 30	77.9×	2.95e-4	6.63e-3 ✓ sig.
sensory perception of sound GJB2, GJB6, POU3F4	GO:0007605	3 / 162	21.6×	3.30e-4	7.16e-3 ✓ sig.
omega-hydroxyceramide biosynthetic process PNPLA1	GO:0106342	1 / 1	1,168×	8.56e-4	1.36e-2 ✓ sig.
mitochondrial ncRNA surveillance SUPV3L1	GO:0035945	1 / 1	1,168×	8.56e-4	1.36e-2 ✓ sig.
mitochondrial mRNA surveillance SUPV3L1	GO:0035946	1 / 1	1,168×	8.56e-4	1.36e-2 ✓ sig.
mitochondrial RNA surveillance SUPV3L1	GO:2000827	1 / 1	1,168×	8.56e-4	1.36e-2 ✓ sig.
cell-cell signaling GJB2, GJB6, GJB3	GO:0007267	3 / 234	15.0×	9.62e-4	1.47e-2 ✓ sig.
urate biosynthetic process PRPS1	GO:0034418	1 / 2	584×	1.71e-3	2.07e-2 ✓ sig.
hypoxanthine biosynthetic process PRPS1	GO:0046101	1 / 2	584×	1.71e-3	2.07e-2 ✓ sig.
keratinocyte activation KRT2	GO:0032980	1 / 2	584×	1.71e-3	2.07e-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	1.64e-12	2.04e-11 ✓ sig.
Deafness, x-linked	X-linked hearing loss with perilymphatic gusher	0.273	3	1.97e-10	2.03e-9 ✓ sig.
Deafness, x-linked	Hearing loss with stapes fixation	0.273	3	1.97e-10	2.03e-9 ✓ sig.
Senter syndrome	X-linked hearing loss with perilymphatic gusher	0.500	2	2.53e-8	2.03e-7 ✓ sig.
Keratitis-ichthyosis-deafness syndrome	Senter syndrome	0.500	2	2.53e-8	2.03e-7 ✓ sig.
Hearing loss with stapes fixation	Senter syndrome	0.500	2	2.53e-8	2.03e-7 ✓ sig.
Keratitis-ichthyosis-deafness syndrome	X-linked hearing loss with perilymphatic gusher	0.400	2	7.59e-8	5.72e-7 ✓ sig.
Hearing loss with stapes fixation	Keratitis-ichthyosis-deafness syndrome	0.400	2	7.59e-8	5.72e-7 ✓ sig.
Deafness, x-linked	Senter syndrome	0.182	2	3.80e-7	2.53e-6 ✓ sig.
Bart-pumphrey syndrome	Keratitis ichthyosis hearing loss syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Bart-pumphrey syndrome	Deafness, digenic	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Keratitis ichthyosis hearing loss syndrome	Vohwinkel syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Keratitis ichthyosis hearing loss syndrome	Senter syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Deafness, digenic	Peripheral neuropathy with sensorineural hearing impairment syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Deafness, digenic	Keratitis ichthyosis hearing loss syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Bart-pumphrey syndrome	Senter syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Clouston syndrome	Senter syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Bart-pumphrey syndrome	Vohwinkel syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Clouston syndrome	X-linked hearing loss with perilymphatic gusher	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Clouston syndrome	Hearing loss with stapes fixation	0.250	1	1.95e-4	5.28e-4 ✓ sig.
ichthyosiform erythroderma, corneal involvement, and hearing loss	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Clouston syndrome	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Keratitis ichthyosis hearing loss syndrome	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Bart-pumphrey syndrome	Keratitis-ichthyosis-deafness syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Deafness, digenic	Senter syndrome	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Senter syndrome	Vohwinkel syndrome	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Deafness, digenic	Vohwinkel syndrome	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Keratitis ichthyosis hearing loss syndrome	Xeroderma	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Bart-pumphrey syndrome	Xeroderma	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Keratitis-ichthyosis-deafness syndrome	Vohwinkel syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Deafness, digenic	Xeroderma	0.167	1	5.19e-4	1.04e-3 ✓ sig.
Senter syndrome	Xeroderma	0.167	1	5.19e-4	1.04e-3 ✓ sig.
Clouston syndrome	Deafness, x-linked	0.091	1	6.49e-4	1.22e-3 ✓ sig.
Deafness, x-linked	X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome	0.091	1	6.49e-4	1.22e-3 ✓ sig.

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