Disease Clusters | GeDiPNet

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Cluster 293

6 diseases · 9 shared-gene connections

6 Diseases

15 Unique genes

0.205 Avg. similarity score

Bulbar palsy Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Episodic ataxia 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.

Episodic ataxia Bulbar palsy Autism, x-linked Central apnea Neonatal encephalopathy Benign paroxysmal torticollis of infancy

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Bulbar palsy	5	5	3
Autism, x-linked	3	3	6
Central apnea	3	3	1
Neonatal encephalopathy	3	3	1
Benign paroxysmal torticollis of infancy	2	2	1
Episodic ataxia	2	2	8

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

Gene ⇵	Member diseases ⇵	Linked diseases
MECP2	4 / 6	Autism, x-linked, Bulbar palsy, Central apnea, Neonatal encephalopathy
CACNA1A	3 / 6	Benign paroxysmal torticollis of infancy, Bulbar palsy, Episodic ataxia

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 ⇵
Presynaptic depolarization and calcium channel opening CACNA1A, CACNB4	Reactome	2 / 12	133×	9.54e-5	2.18e-3 ✓ sig.
Neurexins and neuroligins NLGN3, NLGN4X	Reactome	2 / 32	50.0×	7.07e-4	1.07e-2 ✓ sig.
Loss of MECP2 binding ability to 5hmC-DNA MECP2	Reactome	1 / 1	801×	1.25e-3	1.65e-2 ✓ sig.
Defective SLC1A3 causes episodic ataxia 6 (EA6) SLC1A3	Reactome	1 / 1	801×	1.25e-3	1.65e-2 ✓ sig.
Phase 0 - rapid depolarisation CACNB4, SCN2A	Reactome	2 / 44	36.4×	1.34e-3	1.73e-2 ✓ sig.
Loss of MECP2 binding ability to 5mC-DNA MECP2	Reactome	1 / 3	267×	3.74e-3	3.65e-2 ✓ sig.
Synaptic vesicle cycle CACNA1A, SLC1A3	KEGG	2 / 79	20.3×	4.24e-3	3.98e-2 ✓ sig.
Carnitine synthesis TMLHE	Reactome	1 / 4	200×	4.99e-3	4.44e-2 ✓ sig.
Astrocytic Glutamate-Glutamine Uptake And Metabolism SLC1A3	Reactome	1 / 4	200×	4.99e-3	4.44e-2 ✓ sig.
MECP2 regulates neuronal receptors and channels MECP2	Reactome	1 / 4	200×	4.99e-3	4.44e-2 ✓ sig.
Taste transduction CACNA1A, SCN2A	KEGG	2 / 86	18.6×	5.01e-3	4.45e-2 ✓ sig.
Regulation of MECP2 expression and activity MECP2	Reactome	1 / 6	133×	7.47e-3	5.81e-2
Vitamin B2 (riboflavin) metabolism SLC52A3	Reactome	1 / 7	114×	8.71e-3	6.44e-2
Glutamatergic synapse CACNA1A, SLC1A3	KEGG	2 / 116	13.8×	8.95e-3	6.53e-2
Transport of inorganic cations/anions and amino acids/oligopeptides SLC1A3	Reactome	1 / 8	100×	9.95e-3	6.97e-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 ⇵
chemical synaptic transmission NLGN3, MECP2, PTCHD1, CACNA1A, CACNB4, SLC1A3	GO:0007268	6 / 236	31.7×	1.73e-8	2.72e-6 ✓ sig.
social behavior NLGN3, NLGN4X, MECP2, PTCHD1	GO:0035176	4 / 58	85.9×	1.11e-7	1.34e-5 ✓ sig.
learning NLGN3, NLGN4X, MECP2	GO:0007612	3 / 64	58.4×	1.69e-5	7.99e-4 ✓ sig.
presynaptic membrane assembly NLGN3, NLGN4X	GO:0097105	2 / 9	277×	2.16e-5	9.67e-4 ✓ sig.
regulation of respiratory gaseous exchange by nervous system process NLGN3, MECP2	GO:0002087	2 / 13	192×	4.67e-5	1.74e-3 ✓ sig.
presynapse assembly NLGN3, NLGN4X	GO:0099054	2 / 14	178×	5.44e-5	1.95e-3 ✓ sig.
neuron cell-cell adhesion NLGN3, NLGN4X	GO:0007158	2 / 16	156×	7.17e-5	2.41e-3 ✓ sig.
startle response MECP2, KCNA1	GO:0001964	2 / 18	138×	9.13e-5	2.89e-3 ✓ sig.
vocalization behavior NLGN3, NLGN4X	GO:0071625	2 / 19	131×	1.02e-4	3.14e-3 ✓ sig.
modulation of chemical synaptic transmission NLGN3, NLGN4X, CACNA1A	GO:0050804	3 / 121	30.9×	1.14e-4	3.40e-3 ✓ sig.
monoatomic ion transport CACNA1A, CACNB4, KCNA1, SCN2A, SLC1A3	GO:0006811	5 / 667	9.3×	1.27e-4	3.69e-3 ✓ sig.
monoatomic ion transmembrane transport CACNA1A, CACNB4, KCNA1, SCN2A	GO:0034220	4 / 404	12.3×	2.43e-4	5.89e-3 ✓ sig.
neuronal action potential KCNA1, SCN2A	GO:0019228	2 / 34	73.3×	3.32e-4	7.36e-3 ✓ sig.
long-term memory MECP2, PTCHD1	GO:0007616	2 / 37	67.3×	3.94e-4	8.32e-3 ✓ sig.
adult behavior NLGN3, NLGN4X	GO:0030534	2 / 37	67.3×	3.94e-4	8.32e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Central apnea	Neonatal encephalopathy	0.500	1	6.49e-5	2.32e-4 ✓ sig.
Benign paroxysmal torticollis of infancy	Bulbar palsy	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Bulbar palsy	Central apnea	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Bulbar palsy	Neonatal encephalopathy	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Autism, x-linked	Central apnea	0.143	1	3.90e-4	8.64e-4 ✓ sig.
Autism, x-linked	Neonatal encephalopathy	0.143	1	3.90e-4	8.64e-4 ✓ sig.
Benign paroxysmal torticollis of infancy	Episodic ataxia	0.111	1	5.20e-4	1.06e-3 ✓ sig.
Autism, x-linked	Bulbar palsy	0.111	1	1.17e-3	1.89e-3 ✓ sig.
Bulbar palsy	Episodic ataxia	0.091	1	1.56e-3	2.37e-3 ✓ sig.

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