Disease Clusters | GeDiPNet

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Cluster 357

5 diseases · 9 shared-gene connections

5 Diseases

11 Unique genes

0.327 Avg. similarity score

Adult myoclonic epilepsy Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Benign myoclonic epilepsy 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.

Benign myoclonic epilepsy Adult myoclonic epilepsy Familial adult myoclonic epilepsy Benign adult familial myoclonic epilepsy Early onset epilepsy with developmental delay

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Adult myoclonic epilepsy	4	4	8
Benign myoclonic epilepsy	4	4	6
Familial adult myoclonic epilepsy	4	4	8
Benign adult familial myoclonic epilepsy	3	3	3
Early onset epilepsy with developmental delay	3	3	3

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

Gene ⇵	Member diseases ⇵	Linked diseases
ADRA2B	4 / 5	Adult myoclonic epilepsy, Benign adult familial myoclonic epilepsy, Benign myoclonic epilepsy, Familial adult myoclonic epilepsy
CNTN2	4 / 5	Adult myoclonic epilepsy, Benign myoclonic epilepsy, Early onset epilepsy with developmental delay, Familial adult myoclonic epilepsy
SAMD12	4 / 5	Adult myoclonic epilepsy, Benign adult familial myoclonic epilepsy, Benign myoclonic epilepsy, Familial adult myoclonic epilepsy
MARCHF6	3 / 5	Adult myoclonic epilepsy, Benign myoclonic epilepsy, Familial adult myoclonic epilepsy
YEATS2	3 / 5	Adult myoclonic epilepsy, Benign myoclonic epilepsy, Familial adult myoclonic epilepsy
CTNND2	2 / 5	Adult myoclonic epilepsy, Benign myoclonic epilepsy
RAPGEF2	2 / 5	Adult myoclonic epilepsy, Familial adult myoclonic epilepsy
STARD7	2 / 5	Benign adult familial myoclonic epilepsy, Familial adult myoclonic epilepsy
TNRC6A	2 / 5	Adult myoclonic epilepsy, Familial adult myoclonic epilepsy

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 ⇵
Adrenaline signalling through Alpha-2 adrenergic receptor ADRA2B	Reactome	1 / 3	364×	2.75e-3	2.97e-2 ✓ sig.
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function SETD1A, TNRC6A	Reactome	2 / 97	22.5×	3.39e-3	3.44e-2 ✓ sig.
Post-transcriptional silencing by small RNAs TNRC6A	Reactome	1 / 7	156×	6.40e-3	5.34e-2
Competing endogenous RNAs (ceRNAs) regulate PTEN translation TNRC6A	Reactome	1 / 8	136×	7.31e-3	5.81e-2
Adrenoceptors ADRA2B	Reactome	1 / 9	121×	8.22e-3	6.26e-2
Regulation of PTEN mRNA translation TNRC6A	Reactome	1 / 9	121×	8.22e-3	6.26e-2
Transcriptional Regulation by MECP2 TNRC6A	Reactome	1 / 10	109×	9.12e-3	6.71e-2
Regulation of RUNX1 Expression and Activity TNRC6A	Reactome	1 / 16	68.2×	1.46e-2	8.89e-2
ER Quality Control Compartment (ERQC) MARCHF6	Reactome	1 / 21	52.0×	1.91e-2	1.04e-1
Ion channel transport ATP6V0C	Reactome	1 / 24	45.5×	2.18e-2	1.12e-1
Insulin receptor recycling ATP6V0C	Reactome	1 / 26	42.0×	2.36e-2	1.18e-1
Collecting duct acid secretion ATP6V0C	KEGG	1 / 28	39.0×	2.54e-2	1.22e-1
Synthesis of PC STARD7	Reactome	1 / 28	39.0×	2.54e-2	1.22e-1
Pre-NOTCH Transcription and Translation TNRC6A	Reactome	1 / 31	35.2×	2.80e-2	1.29e-1
Transferrin endocytosis and recycling ATP6V0C	Reactome	1 / 31	35.2×	2.80e-2	1.29e-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 ⇵
establishment of protein localization to juxtaparanode region of axon CNTN2	GO:0071206	1 / 1	1,699×	5.89e-4	1.10e-2 ✓ sig.
presynaptic membrane organization CNTN2	GO:0097090	1 / 1	1,699×	5.89e-4	1.10e-2 ✓ sig.
synapse organization CNTN2, CTNND2	GO:0050808	2 / 72	47.2×	7.87e-4	1.34e-2 ✓ sig.
regulation of astrocyte differentiation CNTN2	GO:0048710	1 / 3	566×	1.76e-3	2.17e-2 ✓ sig.
positive regulation of cAMP-dependent protein kinase activity RAPGEF2	GO:2000481	1 / 3	566×	1.76e-3	2.17e-2 ✓ sig.
positive regulation of adenosine receptor signaling pathway CNTN2	GO:0060168	1 / 3	566×	1.76e-3	2.17e-2 ✓ sig.
myeloid dendritic cell activation STARD7	GO:0001773	1 / 3	566×	1.76e-3	2.17e-2 ✓ sig.
clustering of voltage-gated potassium channels CNTN2	GO:0045163	1 / 4	425×	2.35e-3	2.56e-2 ✓ sig.
protein localization to juxtaparanode region of axon CNTN2	GO:0071205	1 / 4	425×	2.35e-3	2.56e-2 ✓ sig.
cAMP-mediated signaling RAPGEF2	GO:0019933	1 / 4	425×	2.35e-3	2.56e-2 ✓ sig.
positive regulation of dendritic cell apoptotic process RAPGEF2	GO:2000670	1 / 4	425×	2.35e-3	2.56e-2 ✓ sig.
neuron migration CNTN2, RAPGEF2	GO:0001764	2 / 132	25.7×	2.61e-3	2.72e-2 ✓ sig.
negative regulation of epinephrine secretion ADRA2B	GO:0032811	1 / 5	340×	2.94e-3	2.90e-2 ✓ sig.
brain-derived neurotrophic factor receptor signaling pathway RAPGEF2	GO:0031547	1 / 5	340×	2.94e-3	2.90e-2 ✓ sig.
negative regulation of melanin biosynthetic process RAPGEF2	GO:0048022	1 / 5	340×	2.94e-3	2.90e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Adult myoclonic epilepsy	Familial adult myoclonic epilepsy	0.700	7	1.57e-24	3.73e-23 ✓ sig.
Adult myoclonic epilepsy	Benign myoclonic epilepsy	0.667	6	1.51e-21	3.07e-20 ✓ sig.
Benign myoclonic epilepsy	Familial adult myoclonic epilepsy	0.500	5	4.66e-17	7.63e-16 ✓ sig.
Benign adult familial myoclonic epilepsy	Familial adult myoclonic epilepsy	0.333	3	9.21e-11	9.15e-10 ✓ sig.
Benign adult familial myoclonic epilepsy	Benign myoclonic epilepsy	0.250	2	3.80e-7	2.39e-6 ✓ sig.
Adult myoclonic epilepsy	Benign adult familial myoclonic epilepsy	0.200	2	7.08e-7	4.27e-6 ✓ sig.
Benign myoclonic epilepsy	Early onset epilepsy with developmental delay	0.111	1	1.17e-3	1.90e-3 ✓ sig.
Early onset epilepsy with developmental delay	Familial adult myoclonic epilepsy	0.091	1	1.56e-3	2.38e-3 ✓ sig.
Adult myoclonic epilepsy	Early onset epilepsy with developmental delay	0.091	1	1.56e-3	2.38e-3 ✓ sig.

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