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 474

6 diseases · 15 shared-gene connections
6 Diseases
1 Unique genes
0.500 Avg. similarity score
Cataract 46, juvenile-onset 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 ⇵
Cataract 46, juvenile-onset 5 5 1
Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy 5 5 1
Congenital hypoplasia of clavicle 5 5 1
Early progeroid syndrome 5 5 1
Microstomia 5 5 1
Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 5 5 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LEMD2 6 / 6 Cataract 46, juvenile-onset, Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy, Congenital hypoplasia of clavicle, Early progeroid syndrome and 2 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)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Nuclear Envelope Breakdown
LEMD2
 Reactome 1 / 9 1,334× 7.49e-4 9.09e-3 ✓ sig.
Depolymerisation of the Nuclear Lamina
LEMD2
 Reactome 1 / 15 801× 1.25e-3 1.34e-2 ✓ sig.
Initiation of Nuclear Envelope (NE) Reformation
LEMD2
 Reactome 1 / 19 632× 1.58e-3 1.60e-2 ✓ sig.
Sealing of the nuclear envelope (NE) by ESCRT-III
LEMD2
 Reactome 1 / 31 387× 2.58e-3 2.29e-2 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
heart formation
LEMD2
 GO:0060914 1 / 5 3,737× 2.68e-4 6.25e-3 ✓ sig.
nuclear membrane organization
LEMD2
 GO:0071763 1 / 7 2,670× 3.75e-4 7.81e-3 ✓ sig.
nuclear envelope organization
LEMD2
 GO:0006998 1 / 24 779× 1.28e-3 1.67e-2 ✓ sig.
protein localization to chromatin
LEMD2
 GO:0071168 1 / 31 603× 1.66e-3 1.93e-2 ✓ sig.
skeletal muscle cell differentiation
LEMD2
 GO:0035914 1 / 49 381× 2.62e-3 2.44e-2 ✓ sig.
negative regulation of MAPK cascade
LEMD2
 GO:0043409 1 / 64 292× 3.42e-3 2.78e-2 ✓ sig.
negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
LEMD2
 GO:0051898 1 / 78 240× 4.17e-3 3.06e-2 ✓ sig.
neurogenesis
LEMD2
 GO:0022008 1 / 102 183× 5.46e-3 3.47e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cataract 46, juvenile-onset Congenital hypoplasia of clavicle 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset Microstomia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset Early progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy Congenital hypoplasia of clavicle 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy Microstomia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cataract 46, juvenile-onset, with or without arrhythmic cardiomyopathy Early progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hypoplasia of clavicle Microstomia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hypoplasia of clavicle Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital hypoplasia of clavicle Early progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Early progeroid syndrome Microstomia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Early progeroid syndrome Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Microstomia Wormian bones-micrognathia-abnormal dentition-progeroid syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.