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 339

6 diseases · 9 shared-gene connections
6 Diseases
25 Unique genes
0.137 Avg. similarity score
Progressive myoclonic epilepsy Most-connected disease (5 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 ⇵
Progressive myoclonic epilepsy 5 5 24
progressive myoclonus epilepsy 4 4 9
Myoclonus-renal failure syndrome 3 3 1
Unverricht-lundborg syndrome 3 3 3
Progressive myoclonic epilepsy with renal failure 2 2 1
Lafora disease 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCARB2 4 / 6 Myoclonus-renal failure syndrome, Progressive myoclonic epilepsy, progressive myoclonus epilepsy, Unverricht-lundborg syndrome
PRICKLE1 3 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy, Unverricht-lundborg syndrome
SEMA6B 3 / 6 Progressive myoclonic epilepsy, Progressive myoclonic epilepsy with renal failure, progressive myoclonus epilepsy
CERS1 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy
CSTB 2 / 6 Progressive myoclonic epilepsy, Unverricht-lundborg syndrome
GOSR2 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy
KCNC1 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy
KCTD7 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy
NHLRC1 2 / 6 Lafora disease, Progressive myoclonic epilepsy
NUS1 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus epilepsy
SERPINI1 2 / 6 Progressive myoclonic epilepsy, progressive myoclonus 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 ⇵
Myoclonic epilepsy of Lafora
NHLRC1, EPM2A
 Reactome 2 / 9 107× 1.48e-4 3.09e-3 ✓ sig.
Amino acids regulate mTORC1
DEPDC5, NPRL2, NPRL3
 Reactome 3 / 55 26.2× 1.95e-4 3.83e-3 ✓ sig.
Glycogen synthesis
NHLRC1, EPM2A
 Reactome 2 / 16 60.1× 4.90e-4 7.86e-3 ✓ sig.
mTOR signaling pathway
DEPDC5, NPRL2, NPRL3
 KEGG 3 / 158 9.1× 4.15e-3 3.87e-2 ✓ sig.
Defective DHDDS causes retinitis pigmentosa 59
NUS1
 Reactome 1 / 2 240× 4.16e-3 3.87e-2 ✓ sig.
Synthesis of Dolichyl-phosphate
NUS1
 Reactome 1 / 6 80.1× 1.24e-2 7.78e-2
Lysosome
SCARB2, CLN3
 KEGG 2 / 133 7.2× 3.09e-2 1.31e-1
Terpenoid backbone biosynthesis
NUS1
 KEGG 1 / 23 20.9× 4.68e-2 1.65e-1
Wnt signaling pathway
PRICKLE1, PRICKLE2
 KEGG 2 / 174 5.5× 5.04e-2 1.72e-1
SNARE interactions in vesicular transport
GOSR2
 KEGG 1 / 33 14.6× 6.65e-2 1.99e-1
Cargo concentration in the ER
GOSR2
 Reactome 1 / 33 14.6× 6.65e-2 1.99e-1
Sphingolipid de novo biosynthesis
CERS1
 Reactome 1 / 43 11.2× 8.58e-2 2.28e-1
Voltage gated Potassium channels
KCNC1
 Reactome 1 / 43 11.2× 8.58e-2 2.28e-1
Base excision repair
POLG
 KEGG 1 / 44 10.9× 8.78e-2 2.31e-1
Intra-Golgi traffic
GOSR2
 Reactome 1 / 44 10.9× 8.78e-2 2.31e-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 protein localization to plasma membrane
NHLRC1, CLN3, EPM2A
 GO:1903076 3 / 27 83.1× 6.06e-6 3.50e-4 ✓ sig.
cellular response to amino acid starvation
DEPDC5, NPRL2, NPRL3
 GO:0034198 3 / 60 37.4× 6.88e-5 2.29e-3 ✓ sig.
negative regulation of TORC1 signaling
DEPDC5, NPRL2, NPRL3
 GO:1904262 3 / 71 31.6× 1.14e-4 3.33e-3 ✓ sig.
positive regulation of autophagy
DEPDC5, NPRL2, NPRL3
 GO:0010508 3 / 92 24.4× 2.46e-4 5.84e-3 ✓ sig.
glycogen biosynthetic process
NHLRC1, EPM2A
 GO:0005978 2 / 18 83.1× 2.59e-4 6.07e-3 ✓ sig.
regulation of protein ubiquitination
NHLRC1, EPM2A
 GO:0031396 2 / 21 71.2× 3.55e-4 7.52e-3 ✓ sig.
negative regulation of proteolysis
CLN3, CSTB
 GO:0045861 2 / 27 55.4× 5.91e-4 1.07e-2 ✓ sig.
negative regulation of TOR signaling
NPRL3, EPM2A
 GO:0032007 2 / 33 45.3× 8.84e-4 1.39e-2 ✓ sig.
protein localization to lysosome
DEPDC5, NPRL2
 GO:0061462 2 / 33 45.3× 8.84e-4 1.39e-2 ✓ sig.
Wnt signaling pathway, planar cell polarity pathway
PRICKLE1, PRICKLE2
 GO:0060071 2 / 34 44.0× 9.39e-4 1.46e-2 ✓ sig.
glycogen metabolic process
NHLRC1, EPM2A
 GO:0005977 2 / 40 37.4× 1.30e-3 1.76e-2 ✓ sig.
polarized secretion of basement membrane proteins in epithelium
PRICKLE1
 GO:0061865 1 / 1 747× 1.34e-3 1.79e-2 ✓ sig.
anterior visceral endoderm cell migration
PRICKLE1
 GO:1905070 1 / 1 747× 1.34e-3 1.79e-2 ✓ sig.
negative regulation of cardiac muscle cell myoblast differentiation
PRICKLE1
 GO:2000691 1 / 1 747× 1.34e-3 1.79e-2 ✓ sig.
regulation of carbohydrate catabolic process
SCARB2
 GO:0043470 1 / 1 747× 1.34e-3 1.79e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Progressive myoclonic epilepsy progressive myoclonus epilepsy 0.360 9 9.77e-27 2.78e-25 ✓ sig.
Progressive myoclonic epilepsy Unverricht-lundborg syndrome 0.120 3 3.33e-9 3.01e-8 ✓ sig.
progressive myoclonus epilepsy Unverricht-lundborg syndrome 0.182 2 9.11e-7 5.67e-6 ✓ sig.
Myoclonus-renal failure syndrome Unverricht-lundborg syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Myoclonus-renal failure syndrome progressive myoclonus epilepsy 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Progressive myoclonic epilepsy with renal failure progressive myoclonus epilepsy 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Myoclonus-renal failure syndrome Progressive myoclonic epilepsy 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Progressive myoclonic epilepsy Progressive myoclonic epilepsy with renal failure 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Lafora disease Progressive myoclonic epilepsy 0.038 1 3.11e-3 4.09e-3 ✓ sig.