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 541

5 diseases · 10 shared-gene connections
5 Diseases
3 Unique genes
0.400 Avg. similarity score
Amish nemaline myopathy 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 ⇵
Amish nemaline myopathy 4 4 1
Childhood-onset nemaline myopathy 4 4 3
Nemaline myopathy 5 4 4 1
Nemaline myopathy 5a, autosomal recessive, severe infantile 4 4 1
Nemaline myopathy 5c, autosomal dominant 4 4 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TNNT1 5 / 5 Amish nemaline myopathy, Childhood-onset nemaline myopathy, Nemaline myopathy 5, Nemaline myopathy 5a, autosomal recessive, severe infantile 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)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Cytoskeleton in muscle cells
TNNT1, TNNI1, MYPN
 KEGG 3 / 232 51.8× 7.12e-6 2.20e-4 ✓ sig.
Striated Muscle Contraction
TNNT1, TNNI1
 Reactome 2 / 36 222× 2.62e-5 6.51e-4 ✓ sig.
Motor proteins
TNNT1, TNNI1
 KEGG 2 / 194 41.3× 7.71e-4 9.29e-3 ✓ 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 ⇵
transition between fast and slow fiber
TNNT1, TNNI1
 GO:0014883 2 / 9 1,384× 6.18e-7 5.80e-5 ✓ sig.
skeletal muscle contraction
TNNT1, TNNI1
 GO:0003009 2 / 32 389× 8.51e-6 4.80e-4 ✓ sig.
sarcomere organization
TNNT1, MYPN
 GO:0045214 2 / 43 290× 1.55e-5 7.63e-4 ✓ sig.
slow-twitch skeletal muscle fiber contraction
TNNT1
 GO:0031444 1 / 1 6,229× 1.61e-4 4.34e-3 ✓ sig.
negative regulation of muscle contraction
TNNT1
 GO:0045932 1 / 1 6,229× 1.61e-4 4.34e-3 ✓ sig.
regulation of striated muscle contraction
TNNI1
 GO:0006942 1 / 8 779× 1.28e-3 1.67e-2 ✓ sig.
regulation of muscle contraction
TNNT1
 GO:0006937 1 / 16 389× 2.57e-3 2.40e-2 ✓ sig.
dendrite self-avoidance
MYPN
 GO:0070593 1 / 16 389× 2.57e-3 2.40e-2 ✓ sig.
ventricular cardiac muscle tissue morphogenesis
TNNI1
 GO:0055010 1 / 24 260× 3.85e-3 2.94e-2 ✓ sig.
cardiac muscle contraction
TNNI1
 GO:0060048 1 / 43 145× 6.89e-3 3.90e-2 ✓ sig.
homophilic cell adhesion via plasma membrane adhesion molecules
MYPN
 GO:0007156 1 / 167 37.3× 2.66e-2 7.60e-2
axon guidance
MYPN
 GO:0007411 1 / 192 32.4× 3.05e-2 8.17e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Amish nemaline myopathy Nemaline myopathy 5 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amish nemaline myopathy Nemaline myopathy 5a, autosomal recessive, severe infantile 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amish nemaline myopathy Nemaline myopathy 5c, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nemaline myopathy 5 Nemaline myopathy 5a, autosomal recessive, severe infantile 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nemaline myopathy 5 Nemaline myopathy 5c, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nemaline myopathy 5a, autosomal recessive, severe infantile Nemaline myopathy 5c, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amish nemaline myopathy Childhood-onset nemaline myopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Childhood-onset nemaline myopathy Nemaline myopathy 5 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Childhood-onset nemaline myopathy Nemaline myopathy 5a, autosomal recessive, severe infantile 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Childhood-onset nemaline myopathy Nemaline myopathy 5c, autosomal dominant 0.250 1 1.94e-4 4.41e-4 ✓ sig.