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 51
15
Diseases
71
Unique genes
0.183
Avg. similarity score
Congenital nemaline myopathy
Most-connected disease (8 links)
Disease
Searched: nemaline myopathy 6
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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nemaline myopathy 6
Congenital nemaline myopathy
Nemaline myopathy
Congenital neck anomaly
Deglutition disorder
Distal nebulin myopathy
Nebulin-related myopathy
nemaline myopathy 2
Neuronal ceroid lipofuscinosis
Visual disorder
nemaline myopathy 10
nemaline myopathy 8
nemaline myopathy 9
adult neuronal ceroid lipofuscinosis
nemaline myopathy 7
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital nemaline myopathy | 8 | 8 | 5 |
| Nemaline myopathy | 7 | 7 | 18 |
| Congenital neck anomaly | 6 | 6 | 2 |
| Deglutition disorder | 5 | 5 | 11 |
| Distal nebulin myopathy | 5 | 5 | 1 |
| Nebulin-related myopathy | 5 | 5 | 1 |
| nemaline myopathy 2 | 5 | 5 | 1 |
| Neuronal ceroid lipofuscinosis | 2 | 2 | 31 |
| Visual disorder | 2 | 2 | 20 |
| nemaline myopathy 10 | 2 | 2 | 1 |
| nemaline myopathy 8 | 2 | 2 | 1 |
| nemaline myopathy 9 | 2 | 2 | 1 |
| adult neuronal ceroid lipofuscinosis | 1 | 1 | 2 |
| 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 |
|---|---|---|
| NEB | 7 / 15 | Congenital neck anomaly, Congenital nemaline myopathy, Deglutition disorder, Distal nebulin myopathy and 3 more |
| KLHL40 | 3 / 15 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 8 |
| KLHL41 | 3 / 15 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 9 |
| LMOD3 | 3 / 15 | Congenital nemaline myopathy, Nemaline myopathy, nemaline myopathy 10 |
| RIF1 | 3 / 15 | Congenital neck anomaly, Deglutition disorder, Nemaline myopathy |
| ACTA1 | 2 / 15 | Congenital nemaline myopathy, Nemaline myopathy |
| CFL2 | 2 / 15 | Nemaline myopathy, nemaline myopathy 7 |
| CLN3 | 2 / 15 | Neuronal ceroid lipofuscinosis, Visual disorder |
| CLN5 | 2 / 15 | Neuronal ceroid lipofuscinosis, Visual disorder |
| CLN6 | 2 / 15 | Neuronal ceroid lipofuscinosis, Visual disorder |
| CTSF | 2 / 15 | adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis |
| DNAJC5 | 2 / 15 | adult neuronal ceroid lipofuscinosis, Neuronal ceroid lipofuscinosis |
| KBTBD13 | 2 / 15 | Nemaline myopathy, nemaline myopathy 6 |
| PPT1 | 2 / 15 | Neuronal ceroid lipofuscinosis, Visual disorder |
| TSEN2 | 2 / 15 | Deglutition disorder, Visual disorder |
| TSEN34 | 2 / 15 | Deglutition disorder, Visual disorder |
| TSEN54 | 2 / 15 | Deglutition disorder, Visual disorder |
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 ⇵ |
|---|---|---|---|---|---|
| Striated Muscle Contraction | Reactome | 7 / 36 | 32.9× | 1.36e-9 | 1.53e-7 ✓ sig. |
| Cytoskeleton in muscle cells | KEGG | 12 / 232 | 8.7× | 9.51e-9 | 8.74e-7 ✓ sig. |
| Lysosome | KEGG | 8 / 133 | 10.2× | 1.08e-6 | 5.60e-5 ✓ sig. |
| Motor proteins | KEGG | 8 / 194 | 7.0× | 1.79e-5 | 5.73e-4 ✓ sig. |
| Negative feedback regulation of MAPK pathway | Reactome | 2 / 6 | 56.4× | 5.09e-4 | 8.38e-3 ✓ sig. |
| Suppression of apoptosis | Reactome | 2 / 7 | 48.3× | 7.10e-4 | 1.08e-2 ✓ sig. |
| Regulation of HSF1-mediated heat shock response | Reactome | 4 / 69 | 9.8× | 7.26e-4 | 1.10e-2 ✓ sig. |
| Gastrin-CREB signalling pathway via PKC and MAPK | Reactome | 2 / 9 | 37.6× | 1.21e-3 | 1.62e-2 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 4 / 80 | 8.5× | 1.26e-3 | 1.68e-2 ✓ sig. |
| Apoptosis | KEGG | 5 / 137 | 6.2× | 1.28e-3 | 1.70e-2 ✓ sig. |
| Insulin signaling pathway | KEGG | 5 / 138 | 6.1× | 1.32e-3 | 1.74e-2 ✓ sig. |
| Thyroid cancer | KEGG | 3 / 37 | 13.7× | 1.33e-3 | 1.75e-2 ✓ sig. |
| Apelin signaling pathway | KEGG | 5 / 140 | 6.0× | 1.41e-3 | 1.83e-2 ✓ sig. |
| Activation of the AP-1 family of transcription factors | Reactome | 2 / 10 | 33.8× | 1.50e-3 | 1.92e-2 ✓ sig. |
| Regulation of the apoptosome activity | Reactome | 2 / 10 | 33.8× | 1.50e-3 | 1.92e-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 ⇵ |
|---|---|---|---|---|---|
| lysosome organization | GO:0007040 | 8 / 65 | 32.4× | 1.23e-10 | 3.52e-8 ✓ sig. |
| negative regulation of neuron apoptotic process | GO:0043524 | 9 / 160 | 14.8× | 9.33e-9 | 1.60e-6 ✓ sig. |
| sarcomere organization | GO:0045214 | 6 / 43 | 36.7× | 1.32e-8 | 2.18e-6 ✓ sig. |
| lysosomal lumen acidification | GO:0007042 | 5 / 25 | 52.6× | 3.44e-8 | 4.93e-6 ✓ sig. |
| tRNA-type intron splice site recognition and cleavage | GO:0000379 | 3 / 3 | 263× | 5.26e-8 | 7.12e-6 ✓ sig. |
| macromolecule catabolic process | GO:0009057 | 3 / 3 | 263× | 5.26e-8 | 7.12e-6 ✓ sig. |
| lysosomal protein catabolic process | GO:1905146 | 4 / 16 | 65.8× | 3.36e-7 | 3.45e-5 ✓ sig. |
| mitochondrion organization | GO:0007005 | 7 / 130 | 14.2× | 6.16e-7 | 5.70e-5 ✓ sig. |
| Bergmann glial cell differentiation | GO:0060020 | 3 / 11 | 71.8× | 8.48e-6 | 4.76e-4 ✓ sig. |
| regulation of ATP-dependent activity | GO:0043462 | 2 / 2 | 263× | 1.42e-5 | 7.13e-4 ✓ sig. |
| tRNA splicing, via endonucleolytic cleavage and ligation | GO:0006388 | 3 / 13 | 60.7× | 1.46e-5 | 7.28e-4 ✓ sig. |
| myofibril assembly | GO:0030239 | 3 / 15 | 52.6× | 2.31e-5 | 1.04e-3 ✓ sig. |
| protein catabolic process | GO:0030163 | 5 / 97 | 13.6× | 3.37e-5 | 1.38e-3 ✓ sig. |
| interleukin-34-mediated signaling pathway | GO:0061514 | 2 / 3 | 175× | 4.26e-5 | 1.65e-3 ✓ sig. |
| cardiac neural crest cell development involved in heart development | GO:0061308 | 2 / 3 | 175× | 4.26e-5 | 1.65e-3 ✓ sig. |