Disease Clusters | GeDiPNet

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Cluster 206

8 diseases · 17 shared-gene connections

8 Diseases

8 Unique genes

0.320 Avg. similarity score

Carvajal syndrome Most-connected disease (6 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.

Carvajal syndrome Erythrokeratodermia-cardiomyopathy syndrome arrhythmogenic cardiomyopathy with wooly hair and keratoderma Lethal acantholytic epidermolysis bullosa Ventricular arrhythmia Keratosis palmoplantaris striata

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Carvajal syndrome	6	6	1
Erythrokeratodermia-cardiomyopathy syndrome	6	6	1
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	6	6	1
Lethal acantholytic epidermolysis bullosa	5	5	2
Ventricular arrhythmia	4	4	2
Keratosis palmoplantaris striata	3	3	4
Right ventricular cardiomyopathy	3	3	3
Naxos disease	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
DSP	7 / 8	arrhythmogenic cardiomyopathy with wooly hair and keratoderma, Carvajal syndrome, Erythrokeratodermia-cardiomyopathy syndrome, Keratosis palmoplantaris striata and 3 more
JUP	2 / 8	Lethal acantholytic epidermolysis bullosa, Naxos disease

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 ⇵
Arrhythmogenic right ventricular cardiomyopathy DSP, JUP, LMNA, RYR2	KEGG	4 / 86	69.8×	1.68e-7	1.02e-5 ✓ sig.
Formation of the cornified envelope DSP, DSG1, KRT1, JUP	Reactome	4 / 130	46.2×	8.87e-7	4.39e-5 ✓ sig.
Keratinization DSP, DSG1, KRT1, JUP	Reactome	4 / 152	39.5×	1.66e-6	7.51e-5 ✓ sig.
Cytoskeleton in muscle cells DSP, JUP, LMNA, TTN	KEGG	4 / 232	25.9×	8.94e-6	3.06e-4 ✓ sig.
Apoptotic cleavage of cell adhesion proteins DSP, DSG1	Reactome	2 / 11	273×	2.13e-5	6.29e-4 ✓ sig.
Hypertrophic cardiomyopathy LMNA, TTN, RYR2	KEGG	3 / 99	45.5×	2.95e-5	8.23e-4 ✓ sig.
Dilated cardiomyopathy LMNA, TTN, RYR2	KEGG	3 / 105	42.9×	3.52e-5	9.55e-4 ✓ sig.
Neutrophil degranulation DSP, DSG1, KRT1, JUP	Reactome	4 / 480	12.5×	1.55e-4	3.19e-3 ✓ sig.
Breakdown of the nuclear lamina LMNA	Reactome	1 / 3	500×	2.00e-3	2.28e-2 ✓ sig.
Nuclear Envelope Breakdown LMNA	Reactome	1 / 9	167×	5.98e-3	4.92e-2 ✓ sig.
Depolymerisation of the Nuclear Lamina LMNA	Reactome	1 / 15	100×	9.95e-3	6.82e-2
Initiation of Nuclear Envelope (NE) Reformation LMNA	Reactome	1 / 19	79.0×	1.26e-2	7.85e-2
VEGFR2 mediated vascular permeability JUP	Reactome	1 / 29	51.8×	1.92e-2	1.00e-1
Adherens junctions interactions JUP	Reactome	1 / 32	46.9×	2.11e-2	1.06e-1
Striated Muscle Contraction TTN	Reactome	1 / 36	41.7×	2.37e-2	1.13e-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 ⇵
regulation of ventricular cardiac muscle cell action potential DSP, JUP, RYR2	GO:0098911	3 / 11	637×	8.48e-9	1.49e-6 ✓ sig.
bundle of His cell-Purkinje myocyte adhesion involved in cell communication DSP, JUP	GO:0086073	2 / 6	779×	2.40e-6	1.67e-4 ✓ sig.
cardiac muscle hypertrophy TTN, RYR2	GO:0003300	2 / 13	359×	1.25e-5	6.21e-4 ✓ sig.
peptide cross-linking DSP, KRT1	GO:0018149	2 / 19	246×	2.73e-5	1.14e-3 ✓ sig.
striated muscle contraction TTN, RYR2	GO:0006941	2 / 24	195×	4.41e-5	1.64e-3 ✓ sig.
cell-cell adhesion DSP, DSG1, JUP	GO:0098609	3 / 218	32.1×	8.40e-5	2.66e-3 ✓ sig.
regulation of heart rate by cardiac conduction DSP, JUP	GO:0086091	2 / 43	109×	1.44e-4	3.96e-3 ✓ sig.
cardiac muscle contraction TTN, RYR2	GO:0060048	2 / 43	109×	1.44e-4	3.96e-3 ✓ sig.
skin development DSP, JUP	GO:0043588	2 / 55	84.9×	2.35e-4	5.66e-3 ✓ sig.
intermediate filament organization DSP, KRT1	GO:0045109	2 / 70	66.7×	3.82e-4	7.93e-3 ✓ sig.
establishment of protein localization to endoplasmic reticulum RYR2	GO:0072599	1 / 1	2,336×	4.28e-4	8.59e-3 ✓ sig.
Purkinje myocyte to ventricular cardiac muscle cell signaling RYR2	GO:0086029	1 / 2	1,168×	8.56e-4	1.36e-2 ✓ sig.
DNA double-strand break attachment to nuclear envelope LMNA	GO:1990683	1 / 2	1,168×	8.56e-4	1.36e-2 ✓ sig.
regulation of atrial cardiac muscle cell action potential RYR2	GO:0098910	1 / 3	779×	1.28e-3	1.75e-2 ✓ sig.
skeletal muscle myosin thick filament assembly TTN	GO:0030241	1 / 3	779×	1.28e-3	1.75e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Erythrokeratodermia-cardiomyopathy syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Carvajal syndrome	Erythrokeratodermia-cardiomyopathy syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Carvajal syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Lethal acantholytic epidermolysis bullosa	0.333	1	1.30e-4	3.90e-4 ✓ sig.
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Ventricular arrhythmia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Lethal acantholytic epidermolysis bullosa	Naxos disease	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Carvajal syndrome	Lethal acantholytic epidermolysis bullosa	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Carvajal syndrome	Ventricular arrhythmia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Erythrokeratodermia-cardiomyopathy syndrome	Lethal acantholytic epidermolysis bullosa	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Erythrokeratodermia-cardiomyopathy syndrome	Ventricular arrhythmia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Carvajal syndrome	Right ventricular cardiomyopathy	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Erythrokeratodermia-cardiomyopathy syndrome	Right ventricular cardiomyopathy	0.250	1	1.95e-4	5.28e-4 ✓ sig.
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Right ventricular cardiomyopathy	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Lethal acantholytic epidermolysis bullosa	Ventricular arrhythmia	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Carvajal syndrome	Keratosis palmoplantaris striata	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Erythrokeratodermia-cardiomyopathy syndrome	Keratosis palmoplantaris striata	0.200	1	2.60e-4	6.40e-4 ✓ sig.
arrhythmogenic cardiomyopathy with wooly hair and keratoderma	Keratosis palmoplantaris striata	0.200	1	2.60e-4	6.40e-4 ✓ sig.

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