Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 624

5 diseases · 10 shared-gene connections
5 Diseases
1 Unique genes
0.500 Avg. similarity score
Congenital myasthenic syndrome 2A Most-connected disease (4 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Congenital myasthenic syndrome 2A 4 4 1
Congenital myasthenic syndrome 2C 4 4 1
Congenital myasthenic syndrome, biallelic 4 4 1
Congenital myasthenic syndrome, monoallelic 4 4 1
Myasthenic syndrome, congenital, 2c, associated with acetylcholine receptor deficiency 4 4 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CHRNB1 5 / 5 Congenital myasthenic syndrome 2A, Congenital myasthenic syndrome 2C, Congenital myasthenic syndrome, biallelic, Congenital myasthenic syndrome, monoallelic and 1 more
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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Neuroactive ligand-receptor interaction
CHRNB1
 KEGG 1 / 370 32.5× 3.08e-2 1.10e-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 ⇵
postsynaptic membrane organization
CHRNB1
 GO:0001941 1 / 2 9,344× 1.07e-4 3.25e-3 ✓ sig.
behavioral response to nicotine
CHRNB1
 GO:0035095 1 / 9 2,076× 4.82e-4 9.24e-3 ✓ sig.
muscle cell development
CHRNB1
 GO:0055001 1 / 23 812× 1.23e-3 1.64e-2 ✓ sig.
synaptic transmission, cholinergic
CHRNB1
 GO:0007271 1 / 25 747× 1.34e-3 1.71e-2 ✓ sig.
acetylcholine receptor signaling pathway
CHRNB1
 GO:0095500 1 / 28 667× 1.50e-3 1.82e-2 ✓ sig.
neuromuscular synaptic transmission
CHRNB1
 GO:0007274 1 / 31 603× 1.66e-3 1.93e-2 ✓ sig.
membrane depolarization
CHRNB1
 GO:0051899 1 / 32 584× 1.71e-3 1.96e-2 ✓ sig.
skeletal muscle contraction
CHRNB1
 GO:0003009 1 / 32 584× 1.71e-3 1.96e-2 ✓ sig.
nervous system process
CHRNB1
 GO:0050877 1 / 53 353× 2.84e-3 2.54e-2 ✓ sig.
regulation of postsynaptic membrane potential
CHRNB1
 GO:0060078 1 / 59 317× 3.16e-3 2.69e-2 ✓ sig.
monoatomic cation transport
CHRNB1
 GO:0006812 1 / 61 306× 3.26e-3 2.72e-2 ✓ sig.
excitatory postsynaptic potential
CHRNB1
 GO:0060079 1 / 69 271× 3.69e-3 2.89e-2 ✓ sig.
regulation of membrane potential
CHRNB1
 GO:0042391 1 / 85 220× 4.55e-3 3.20e-2 ✓ sig.
muscle contraction
CHRNB1
 GO:0006936 1 / 85 220× 4.55e-3 3.20e-2 ✓ sig.
monoatomic ion transmembrane transport
CHRNB1
 GO:0034220 1 / 404 46.3× 2.16e-2 6.78e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital myasthenic syndrome 2A Congenital myasthenic syndrome 2C 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2A Congenital myasthenic syndrome, monoallelic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2A Congenital myasthenic syndrome, biallelic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2A Myasthenic syndrome, congenital, 2c, associated with acetylcholine receptor deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2C Congenital myasthenic syndrome, monoallelic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2C Congenital myasthenic syndrome, biallelic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome 2C Myasthenic syndrome, congenital, 2c, associated with acetylcholine receptor deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome, biallelic Congenital myasthenic syndrome, monoallelic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome, biallelic Myasthenic syndrome, congenital, 2c, associated with acetylcholine receptor deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myasthenic syndrome, monoallelic Myasthenic syndrome, congenital, 2c, associated with acetylcholine receptor deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.