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 58

15 diseases · 41 shared-gene connections
15 Diseases
30 Unique genes
0.114 Avg. similarity score
Muscle eye brain disease Most-connected disease (14 links)
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Disease Searched: myopathy caused by variation in POMGNT1 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 ⇵
Muscle eye brain disease 14 14 15
Walker-warburg syndrome 14 14 16
Congenital muscular dystrophy 11 11 22
Congenital muscular dystrophy due to dystroglycanopathy 8 8 7
muscular dystrophy-dystroglycanopathy 4 4 1
myopathy caused by variation in CRPPA 4 4 1
myopathy caused by variation in FKRP 4 4 1
myopathy caused by variation in GMPPB 4 4 1
myopathy caused by variation in POMGNT1 4 4 1
myopathy caused by variation in FKTN 3 3 1
myopathy caused by variation in POMT1 3 3 1
myopathy caused by variation in POMT2 3 3 1
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 2 2 1
myopathy caused by variation in POMGNT2 2 2 1
neuromuscular disease caused by qualitative or quantitative defects of alpha-dystroglycan 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CRPPA 5 / 15 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, myopathy caused by variation in CRPPA and 1 more
FKRP 5 / 15 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, myopathy caused by variation in FKRP and 1 more
GMPPB 5 / 15 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, myopathy caused by variation in GMPPB and 1 more
LARGE1 5 / 15 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, muscular dystrophy-dystroglycanopathy and 1 more
POMGNT1 5 / 15 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, myopathy caused by variation in POMGNT1 and 1 more
FKTN 4 / 15 Congenital muscular dystrophy, Muscle eye brain disease, myopathy caused by variation in FKTN, Walker-warburg syndrome
POMT1 4 / 15 Congenital muscular dystrophy, Muscle eye brain disease, myopathy caused by variation in POMT1, Walker-warburg syndrome
POMT2 4 / 15 Congenital muscular dystrophy, Muscle eye brain disease, myopathy caused by variation in POMT2, Walker-warburg syndrome
B3GALNT2 3 / 15 Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Walker-warburg syndrome
B4GAT1 3 / 15 Muscle eye brain disease, muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13, Walker-warburg syndrome
DAG1 3 / 15 Muscle eye brain disease, neuromuscular disease caused by qualitative or quantitative defects of alpha-dystroglycan, Walker-warburg syndrome
POMGNT2 3 / 15 Muscle eye brain disease, myopathy caused by variation in POMGNT2, Walker-warburg syndrome
POMK 3 / 15 Congenital muscular dystrophy, Muscle eye brain disease, Walker-warburg syndrome
RXYLT1 2 / 15 Muscle eye brain disease, Walker-warburg syndrome
TSPAN1 2 / 15 Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease
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 ⇵
Mannose type O-glycan biosynthesis
B3GALNT2, CRPPA, FKRP, LARGE1, POMGNT1, POMT1, POMK, POMT2, FKTN, B4GAT1, POMGNT2, RXYLT1
 KEGG 12 / 23 209× 6.16e-27 1.22e-23 ✓ sig.
O-linked glycosylation
B3GALNT2, LARGE1, POMGNT1, POMT1, POMK, POMT2, B4GAT1, DAG1, POMGNT2
 Reactome 9 / 10 360× 1.00e-23 1.28e-20 ✓ sig.
Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2
POMT1, POMT2, DAG1
 Reactome 3 / 3 400× 1.41e-8 1.11e-6 ✓ sig.
Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1
POMT1, POMT2, DAG1
 Reactome 3 / 3 400× 1.41e-8 1.11e-6 ✓ sig.
Cytoskeleton in muscle cells
CAPN3, COL6A2, LAMA2, LMNA, NEB, ITGA7, DAG1, COL4A1
 KEGG 8 / 232 13.8× 6.97e-8 4.62e-6 ✓ sig.
Metabolic pathways
B3GALNT2, CRPPA, FKRP, GMPPB, LARGE1, POMGNT1, POMT1, INPP5K, POMK, POMT2, DPM2, FKTN
 KEGG 15 / 1,563 3.8× 1.11e-6 5.11e-5 ✓ sig.
ECM-receptor interaction
COL6A2, LAMA2, ITGA7, DAG1, COL4A1
 KEGG 5 / 89 22.5× 2.46e-6 1.01e-4 ✓ sig.
Defective LARGE causes MDDGA6 and MDDGB6
LARGE1, B4GAT1
 Reactome 2 / 2 400× 6.03e-6 2.13e-4 ✓ sig.
Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3
POMGNT1, DAG1
 Reactome 2 / 2 400× 6.03e-6 2.13e-4 ✓ sig.
Laminin interactions
LAMA2, ITGA7, COL4A1
 Reactome 3 / 28 42.9× 4.42e-5 1.12e-3 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 86 18.6× 5.83e-5 1.40e-3 ✓ sig.
Hypertrophic cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 99 16.2× 1.01e-4 2.21e-3 ✓ sig.
Dilated cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 105 15.3× 1.27e-4 2.64e-3 ✓ sig.
ECM proteoglycans
COL6A2, ITGA7, DAG1
 Reactome 3 / 51 23.5× 2.70e-4 4.83e-3 ✓ sig.
NCAM1 interactions
COL6A2, COL4A1
 Reactome 2 / 21 38.1× 1.23e-3 1.58e-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 ⇵
protein O-linked glycosylation via mannose
CRPPA, FKRP, LARGE1, POMGNT1, POMT1, POMT2, FKTN, B4GAT1, POMGNT2, RXYLT1
 GO:0035269 10 / 18 346× 9.14e-25 2.93e-21 ✓ sig.
protein glycosylation
B3GALNT2, CRPPA, FKRP, GMPPB, LARGE1, POMGNT1, POMT1, POMT2, DPM2, FKTN, B4GAT1, POMGNT2
 GO:0006486 13 / 181 44.7× 4.43e-19 6.05e-16 ✓ sig.
basement membrane organization
FKRP, LARGE1, POMGNT1, POMT2, FKTN, DAG1, COL4A1
 GO:0071711 7 / 29 150× 1.97e-14 1.23e-11 ✓ sig.
protein O-linked glycosylation
B3GALNT2, LARGE1, POMGNT1, POMT1, POMK, POMT2, FKTN, POMGNT2
 GO:0006493 8 / 71 70.2× 1.58e-13 8.29e-11 ✓ sig.
muscle organ development
LARGE1, CAPN3, LAMA2, LMNA, NEB, ITGA7, FKTN
 GO:0007517 7 / 114 38.2× 4.73e-10 1.16e-7 ✓ sig.
localization of cell
FKRP, LARGE1, POMGNT1
 GO:0051674 3 / 6 311× 7.44e-8 9.32e-6 ✓ sig.
reactive gliosis
LARGE1, POMGNT1, POMT2
 GO:0150103 3 / 6 311× 7.44e-8 9.32e-6 ✓ sig.
skeletal muscle fiber differentiation
FKRP, LARGE1, FKTN
 GO:0098528 3 / 9 208× 3.12e-7 3.15e-5 ✓ sig.
brain development
FKRP, LARGE1, POMGNT1, POMK, FKTN, COL4A1
 GO:0007420 6 / 244 15.3× 2.13e-6 1.52e-4 ✓ sig.
glycoprotein metabolic process
FKRP, LARGE1, FKTN
 GO:0009100 3 / 22 84.9× 5.63e-6 3.33e-4 ✓ sig.
skeletal muscle tissue regeneration
FKRP, LARGE1, DAG1
 GO:0043403 3 / 26 71.9× 9.47e-6 5.05e-4 ✓ sig.
dentate gyrus development
LARGE1, POMGNT1, POMT2
 GO:0021542 3 / 26 71.9× 9.47e-6 5.05e-4 ✓ sig.
regulation of myoblast differentiation
CAPN3, TRIP4
 GO:0045661 2 / 6 208× 3.72e-5 1.45e-3 ✓ sig.
neuromuscular process
FKRP, LARGE1, POMK
 GO:0050905 3 / 42 44.5× 4.11e-5 1.56e-3 ✓ sig.
connective tissue development
FKRP, LARGE1
 GO:0061448 2 / 7 178× 5.21e-5 1.86e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Muscle eye brain disease Walker-warburg syndrome 0.778 14 3.75e-45 1.76e-43 ✓ sig.
Congenital muscular dystrophy Muscle eye brain disease 0.310 9 1.85e-23 4.15e-22 ✓ sig.
Congenital muscular dystrophy Walker-warburg syndrome 0.300 9 4.23e-23 9.26e-22 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy Muscle eye brain disease 0.438 7 1.58e-22 3.36e-21 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy Walker-warburg syndrome 0.333 6 3.03e-18 5.27e-17 ✓ sig.
Congenital muscular dystrophy Congenital muscular dystrophy due to dystroglycanopathy 0.200 5 7.66e-14 9.99e-13 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy myopathy caused by variation in POMGNT1 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy myopathy caused by variation in FKRP 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy myopathy caused by variation in CRPPA 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy muscular dystrophy-dystroglycanopathy 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy myopathy caused by variation in GMPPB 0.125 1 4.55e-4 9.72e-4 ✓ sig.
Muscle eye brain disease neuromuscular disease caused by qualitative or quantitative defects of alpha-dystroglycan 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in POMGNT1 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in GMPPB 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in POMGNT2 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in FKTN 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in POMT1 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in FKRP 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in POMT2 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease myopathy caused by variation in CRPPA 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Muscle eye brain disease muscular dystrophy-dystroglycanopathy 0.063 1 9.74e-4 1.66e-3 ✓ sig.
myopathy caused by variation in POMT1 Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in POMGNT2 Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in POMT2 Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in POMGNT1 Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
neuromuscular disease caused by qualitative or quantitative defects of alpha-dystroglycan Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in GMPPB Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in FKTN Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in FKRP Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
myopathy caused by variation in CRPPA Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
muscular dystrophy-dystroglycanopathy Walker-warburg syndrome 0.059 1 1.04e-3 1.74e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in GMPPB 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in FKTN 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in POMGNT1 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in FKRP 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in CRPPA 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in POMT1 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy myopathy caused by variation in POMT2 0.043 1 1.43e-3 2.23e-3 ✓ sig.
Congenital muscular dystrophy muscular dystrophy-dystroglycanopathy 0.043 1 1.43e-3 2.23e-3 ✓ sig.