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 357

7 diseases · 15 shared-gene connections
7 Diseases
32 Unique genes
0.244 Avg. similarity score
Muscle eye brain disease Most-connected disease (6 links)
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Disease Searched: Myopathy caused by variation in CRPPA 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 6 6 15
Walker-warburg syndrome 6 6 16
Congenital muscular dystrophy 5 5 23
Congenital muscular dystrophy due to dystroglycanopathy 4 4 7
Myopathy caused by variation in CRPPA 4 4 1
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a 3 3 6
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a13 2 2 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
CRPPA 5 / 7 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Myopathy caused by variation in CRPPA and 1 more
POMGNT1 5 / 7 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a and 1 more
FKRP 4 / 7 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Walker-warburg syndrome
FKTN 4 / 7 Congenital muscular dystrophy, Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, Walker-warburg syndrome
GMPPB 4 / 7 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Walker-warburg syndrome
LARGE1 4 / 7 Congenital muscular dystrophy, Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Walker-warburg syndrome
POMK 4 / 7 Congenital muscular dystrophy, Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, Walker-warburg syndrome
POMT1 4 / 7 Congenital muscular dystrophy, Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, Walker-warburg syndrome
POMT2 4 / 7 Congenital muscular dystrophy, Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, Walker-warburg syndrome
B3GALNT2 3 / 7 Congenital muscular dystrophy due to dystroglycanopathy, Muscle eye brain disease, Walker-warburg syndrome
B4GAT1 3 / 7 Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a13, Walker-warburg syndrome
DAG1 3 / 7 Muscle eye brain disease, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, Walker-warburg syndrome
POMGNT2 2 / 7 Muscle eye brain disease, Walker-warburg syndrome
RXYLT1 2 / 7 Muscle eye brain disease, Walker-warburg syndrome
TSPAN1 2 / 7 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 / 23 196× 1.61e-26 3.37e-23 ✓ sig.
O-linked glycosylation
B3GALNT2, LARGE1, POMGNT1, POMT1, POMK, POMT2, B4GAT1, DAG1, POMGNT2
 Reactome 9 / 10 338× 1.96e-23 2.64e-20 ✓ sig.
Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2
POMT1, POMT2, DAG1
 Reactome 3 / 3 375× 1.72e-8 1.19e-6 ✓ sig.
Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1
POMT1, POMT2, DAG1
 Reactome 3 / 3 375× 1.72e-8 1.19e-6 ✓ sig.
Cytoskeleton in muscle cells
CAPN3, COL6A2, LAMA2, LMNA, NEB, ITGA7, DAG1, COL4A1
 KEGG 8 / 232 12.9× 1.21e-7 6.62e-6 ✓ sig.
Metabolic pathways
B3GALNT2, CRPPA, FKRP, GMPPB, LARGE1, POMGNT1, POMT1, INPP5K, POMK, POMT2, DPM2, FKTN
 KEGG 16 / 1,563 3.8× 4.83e-7 2.22e-5 ✓ sig.
ECM-receptor interaction
COL6A2, LAMA2, ITGA7, DAG1, COL4A1
 KEGG 5 / 89 21.1× 3.43e-6 1.20e-4 ✓ sig.
Defective LARGE causes MDDGA6 and MDDGB6
LARGE1, B4GAT1
 Reactome 2 / 2 375× 6.88e-6 2.13e-4 ✓ sig.
Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3
POMGNT1, DAG1
 Reactome 2 / 2 375× 6.88e-6 2.13e-4 ✓ sig.
Laminin interactions
LAMA2, ITGA7, COL4A1
 Reactome 3 / 28 40.2× 5.38e-5 1.15e-3 ✓ sig.
Arrhythmogenic right ventricular cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 86 17.5× 7.56e-5 1.52e-3 ✓ sig.
Hypertrophic cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 99 15.2× 1.31e-4 2.34e-3 ✓ sig.
Dilated cardiomyopathy
LAMA2, LMNA, ITGA7, DAG1
 KEGG 4 / 105 14.3× 1.64e-4 2.81e-3 ✓ sig.
ECM proteoglycans
COL6A2, ITGA7, DAG1
 Reactome 3 / 51 22.1× 3.28e-4 4.82e-3 ✓ sig.
NCAM1 interactions
COL6A2, COL4A1
 Reactome 2 / 21 35.7× 1.40e-3 1.46e-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 / 18 324× 1.96e-24 5.53e-21 ✓ sig.
protein glycosylation
B3GALNT2, CRPPA, FKRP, GMPPB, LARGE1, POMGNT1, POMT1, POMT2, DPM2, FKTN, B4GAT1, POMGNT2
 GO:0006486 14 / 181 45.2× 1.56e-20 2.67e-17 ✓ sig.
protein O-linked glycosylation
B3GALNT2, LARGE1, POMGNT1, POMT1, POMK, POMT2, FKTN, POMGNT2, B3GNT2
 GO:0006493 9 / 71 74.0× 2.55e-15 1.93e-12 ✓ sig.
basement membrane organization
FKRP, LARGE1, POMGNT1, POMT2, FKTN, DAG1, COL4A1
 GO:0071711 7 / 29 141× 3.25e-14 2.05e-11 ✓ sig.
muscle organ development
LARGE1, CAPN3, LAMA2, LMNA, NEB, ITGA7, FKTN
 GO:0007517 7 / 114 35.9× 7.75e-10 1.86e-7 ✓ sig.
localization of cell
FKRP, LARGE1, POMGNT1
 GO:0051674 3 / 6 292× 9.09e-8 1.17e-5 ✓ sig.
reactive gliosis
LARGE1, POMGNT1, POMT2
 GO:0150103 3 / 6 292× 9.09e-8 1.17e-5 ✓ sig.
skeletal muscle fiber differentiation
FKRP, LARGE1, FKTN
 GO:0098528 3 / 9 195× 3.80e-7 3.86e-5 ✓ sig.
brain development
FKRP, LARGE1, POMGNT1, POMK, FKTN, COL4A1
 GO:0007420 6 / 244 14.4× 3.18e-6 2.20e-4 ✓ sig.
glycoprotein metabolic process
FKRP, LARGE1, FKTN
 GO:0009100 3 / 22 79.6× 6.87e-6 4.06e-4 ✓ sig.
skeletal muscle tissue regeneration
FKRP, LARGE1, DAG1
 GO:0043403 3 / 26 67.4× 1.15e-5 6.08e-4 ✓ sig.
dentate gyrus development
LARGE1, POMGNT1, POMT2
 GO:0021542 3 / 26 67.4× 1.15e-5 6.08e-4 ✓ sig.
axon guidance
CRPPA, LAMA2, B4GAT1, DAG1, B3GNT2
 GO:0007411 5 / 192 15.2× 1.75e-5 8.35e-4 ✓ sig.
regulation of myoblast differentiation
CAPN3, TRIP4
 GO:0045661 2 / 6 195× 4.24e-5 1.63e-3 ✓ sig.
neuromuscular process
FKRP, LARGE1, POMK
 GO:0050905 3 / 42 41.7× 5.00e-5 1.85e-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 3.45e-45 8.68e-44 ✓ sig.
Congenital muscular dystrophy Muscle eye brain disease 0.300 9 2.89e-23 4.68e-22 ✓ sig.
Congenital muscular dystrophy Walker-warburg syndrome 0.290 9 6.59e-23 1.05e-21 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy Muscle eye brain disease 0.438 7 1.52e-22 2.41e-21 ✓ sig.
Muscle eye brain disease Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a 0.375 6 2.61e-19 3.72e-18 ✓ sig.
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a Walker-warburg syndrome 0.353 6 4.18e-19 5.93e-18 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy Walker-warburg syndrome 0.333 6 2.93e-18 4.03e-17 ✓ sig.
Congenital muscular dystrophy Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a 0.200 5 2.72e-14 3.18e-13 ✓ sig.
Congenital muscular dystrophy Congenital muscular dystrophy due to dystroglycanopathy 0.192 5 9.50e-14 1.07e-12 ✓ sig.
Congenital muscular dystrophy due to dystroglycanopathy Myopathy caused by variation in CRPPA 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Muscle eye brain disease Myopathy caused by variation in CRPPA 0.063 1 9.68e-4 1.50e-3 ✓ sig.
Myopathy caused by variation in CRPPA Walker-warburg syndrome 0.059 1 1.03e-3 1.57e-3 ✓ sig.
Congenital muscular dystrophy Myopathy caused by variation in CRPPA 0.042 1 1.49e-3 2.12e-3 ✓ sig.
Muscle eye brain disease Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a13 0.059 1 1.94e-3 2.65e-3 ✓ sig.
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a13 Walker-warburg syndrome 0.056 1 2.07e-3 2.79e-3 ✓ sig.