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 162
9
Diseases
18
Unique genes
0.155
Avg. similarity score
Congenital nemaline myopathy
Most-connected disease (6 links)
Disease
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Congenital nemaline myopathy
Nemaline myopathy
Alpha-actinopathy
Zebra body myopathy
nemaline myopathy 10
nemaline myopathy 8
nemaline myopathy 9
nemaline myopathy 6
nemaline myopathy 7
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital nemaline myopathy | 6 | 6 | 5 |
| Nemaline myopathy | 6 | 6 | 18 |
| Alpha-actinopathy | 2 | 2 | 1 |
| Zebra body myopathy | 2 | 2 | 1 |
| nemaline myopathy 10 | 2 | 2 | 1 |
| nemaline myopathy 8 | 2 | 2 | 1 |
| nemaline myopathy 9 | 2 | 2 | 1 |
| nemaline myopathy 6 | 1 | 1 | 1 |
| nemaline myopathy 7 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ACTA1 | 4 / 9 | Alpha-actinopathy, Congenital nemaline myopathy, Nemaline myopathy, Zebra body myopathy |
| KLHL40 | 3 / 9 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 8 |
| KLHL41 | 3 / 9 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 9 |
| LMOD3 | 3 / 9 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 10 |
| CFL2 | 2 / 9 | Nemaline myopathy, nemaline myopathy 7 |
| KBTBD13 | 2 / 9 | Nemaline myopathy, nemaline myopathy 6 |
| NEB | 2 / 9 | Congenital nemaline myopathy, Nemaline myopathy |
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 | KEGG | 11 / 232 | 31.6× | 3.12e-15 | 1.09e-12 ✓ sig. |
| Striated Muscle Contraction | Reactome | 7 / 36 | 130× | 3.64e-14 | 1.00e-11 ✓ sig. |
| Motor proteins | KEGG | 7 / 194 | 24.1× | 7.05e-9 | 6.44e-7 ✓ sig. |
| Smooth Muscle Contraction | Reactome | 2 / 34 | 39.2× | 1.16e-3 | 1.51e-2 ✓ sig. |
| Cardiac muscle contraction | KEGG | 2 / 87 | 15.3× | 7.36e-3 | 5.65e-2 |
| Hypertrophic cardiomyopathy | KEGG | 2 / 99 | 13.5× | 9.44e-3 | 6.63e-2 |
| Dilated cardiomyopathy | KEGG | 2 / 105 | 12.7× | 1.06e-2 | 7.11e-2 |
| Cell-extracellular matrix interactions | Reactome | 1 / 12 | 55.6× | 1.78e-2 | 9.67e-2 |
| Adrenergic signaling in cardiomyocytes | KEGG | 2 / 154 | 8.7× | 2.18e-2 | 1.08e-1 |
| Cholesterol biosynthesis | Reactome | 1 / 21 | 31.8× | 3.10e-2 | 1.31e-1 |
| Terpenoid backbone biosynthesis | KEGG | 1 / 23 | 29.0× | 3.39e-2 | 1.38e-1 |
| Neddylation | Reactome | 2 / 234 | 5.7× | 4.71e-2 | 1.66e-1 |
| Thyroid cancer | KEGG | 1 / 37 | 18.0× | 5.41e-2 | 1.79e-1 |
| Activation of gene expression by SREBF (SREBP) | Reactome | 1 / 42 | 15.9× | 6.12e-2 | 1.90e-1 |
| Antigen processing: Ubiquitination & Proteasome degradation | Reactome | 2 / 309 | 4.3× | 7.70e-2 | 2.15e-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 ⇵ |
|---|---|---|---|---|---|
| sarcomere organization | GO:0045214 | 6 / 43 | 145× | 1.88e-12 | 8.09e-10 ✓ sig. |
| actin filament organization | GO:0007015 | 5 / 152 | 34.2× | 2.62e-7 | 2.72e-5 ✓ sig. |
| regulation of ATP-dependent activity | GO:0043462 | 2 / 2 | 1,038× | 8.76e-7 | 7.44e-5 ✓ sig. |
| muscle contraction | GO:0006936 | 4 / 85 | 48.9× | 1.16e-6 | 9.35e-5 ✓ sig. |
| striated muscle contraction | GO:0006941 | 3 / 24 | 130× | 1.50e-6 | 1.15e-4 ✓ sig. |
| skeletal muscle fiber development | GO:0048741 | 3 / 31 | 100× | 3.32e-6 | 2.17e-4 ✓ sig. |
| skeletal muscle contraction | GO:0003009 | 3 / 32 | 97.3× | 3.66e-6 | 2.34e-4 ✓ sig. |
| skeletal muscle thin filament assembly | GO:0030240 | 2 / 6 | 346× | 1.31e-5 | 6.45e-4 ✓ sig. |
| regulation of striated muscle contraction | GO:0006942 | 2 / 8 | 260× | 2.45e-5 | 1.05e-3 ✓ sig. |
| transition between fast and slow fiber | GO:0014883 | 2 / 9 | 231× | 3.14e-5 | 1.27e-3 ✓ sig. |
| myofibril assembly | GO:0030239 | 2 / 15 | 138× | 9.13e-5 | 2.83e-3 ✓ sig. |
| regulation of muscle contraction | GO:0006937 | 2 / 16 | 130× | 1.04e-4 | 3.12e-3 ✓ sig. |
| positive regulation of calcium-dependent ATPase activity | GO:1903612 | 1 / 1 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| slow-twitch skeletal muscle fiber contraction | GO:0031444 | 1 / 1 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| negative regulation of muscle contraction | GO:0045932 | 1 / 1 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital nemaline myopathy | Nemaline myopathy | 0.263 | 5 | 1.19e-15 | 1.87e-14 ✓ sig. |
| Alpha-actinopathy | Zebra body myopathy | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Alpha-actinopathy | Congenital nemaline myopathy | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Congenital nemaline myopathy | Zebra body myopathy | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Congenital nemaline myopathy | nemaline myopathy 10 | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Congenital nemaline myopathy | nemaline myopathy 8 | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Congenital nemaline myopathy | nemaline myopathy 9 | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Nemaline myopathy | nemaline myopathy 10 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Nemaline myopathy | nemaline myopathy 6 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Nemaline myopathy | nemaline myopathy 7 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Nemaline myopathy | nemaline myopathy 8 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |
| Nemaline myopathy | nemaline myopathy 9 | 0.053 | 1 | 1.17e-3 | 1.88e-3 ✓ sig. |