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 198
9
Diseases
13
Unique genes
0.314
Avg. similarity score
Growth failure
Most-connected disease (7 links)
Disease
Searched: Skeletal abnormalities
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Skeletal abnormalities
Growth failure
Hepatic disease
Lowry-wood syndrome
Microcephalic osteodysplastic primordial dwarfism
Microcephalic osteodysplastic primordial dwarfism, type i
RNU4ATAC spectrum disorder
Failure to thrive
Microcephalic osteodysplastic primordial dwarfism type II
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Growth failure | 7 | 7 | 2 |
| Hepatic disease | 6 | 6 | 3 |
| Lowry-wood syndrome | 5 | 5 | 1 |
| Microcephalic osteodysplastic primordial dwarfism | 5 | 5 | 3 |
| Microcephalic osteodysplastic primordial dwarfism, type i | 5 | 5 | 1 |
| RNU4ATAC spectrum disorder | 5 | 5 | 1 |
| Failure to thrive | 3 | 3 | 8 |
| Skeletal abnormalities | 3 | 3 | 4 |
| Microcephalic osteodysplastic primordial dwarfism type II | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| RNU4ATAC | 8 / 9 | Failure to thrive, Growth failure, Hepatic disease, Lowry-wood syndrome and 4 more |
| RNU6ATAC | 4 / 9 | Failure to thrive, Growth failure, Hepatic disease, Skeletal abnormalities |
| PCNT | 2 / 9 | Microcephalic osteodysplastic primordial dwarfism, Microcephalic osteodysplastic primordial dwarfism type II |
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 ⇵ |
|---|---|---|---|---|---|
| Defective TCN2 causes hereditary megaloblastic anemia | Reactome | 1 / 1 | 924× | 1.08e-3 | 1.20e-2 ✓ sig. |
| Defective CD320 causes methylmalonic aciduria | Reactome | 1 / 2 | 462× | 2.16e-3 | 2.02e-2 ✓ sig. |
| SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion | Reactome | 1 / 10 | 92.4× | 1.08e-2 | 5.96e-2 |
| Sema3A PAK dependent Axon repulsion | Reactome | 1 / 15 | 61.6× | 1.61e-2 | 7.58e-2 |
| CRMPs in Sema3A signaling | Reactome | 1 / 16 | 57.7× | 1.72e-2 | 7.86e-2 |
| Cobalamin transport and metabolism | KEGG | 1 / 18 | 51.3× | 1.93e-2 | 8.40e-2 |
| Cobalamin (Cbl, vitamin B12) transport and metabolism | Reactome | 1 / 21 | 44.0× | 2.25e-2 | 9.16e-2 |
| Vitamin digestion and absorption | KEGG | 1 / 26 | 35.5× | 2.78e-2 | 1.03e-1 |
| Aggrephagy | Reactome | 1 / 40 | 23.1× | 4.25e-2 | 1.32e-1 |
| Ion transport by P-type ATPases | Reactome | 1 / 56 | 16.5× | 5.90e-2 | 1.59e-1 |
| Pyrimidine metabolism | KEGG | 1 / 58 | 15.9× | 6.10e-2 | 1.62e-1 |
| RNA Polymerase II Transcription Elongation | Reactome | 1 / 59 | 15.7× | 6.20e-2 | 1.64e-1 |
| E3 ubiquitin ligases ubiquitinate target proteins | Reactome | 1 / 59 | 15.7× | 6.20e-2 | 1.64e-1 |
| Formation of RNA Pol II elongation complex | Reactome | 1 / 61 | 15.1× | 6.41e-2 | 1.67e-1 |
| Loss of Nlp from mitotic centrosomes | Reactome | 1 / 70 | 13.2× | 7.32e-2 | 1.80e-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 ⇵ |
|---|---|---|---|---|---|
| mRNA 5'-splice site recognition | GO:0000395 | 2 / 24 | 120× | 1.22e-4 | 3.57e-3 ✓ sig. |
| spliceosomal tri-snRNP complex assembly | GO:0000244 | 2 / 26 | 111× | 1.44e-4 | 4.01e-3 ✓ sig. |
| retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | GO:0006890 | 2 / 50 | 57.5× | 5.37e-4 | 9.91e-3 ✓ sig. |
| protein deadenylylation | GO:0044602 | 1 / 1 | 1,437× | 6.96e-4 | 1.18e-2 ✓ sig. |
| negative regulation of mitotic chromosome condensation | GO:1905213 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| cerebellar granule cell precursor tangential migration | GO:0021935 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| dUDP biosynthetic process | GO:0006227 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| dTDP biosynthetic process | GO:0006233 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| protein adenylylation | GO:0018117 | 1 / 2 | 719× | 1.39e-3 | 1.75e-2 ✓ sig. |
| regulation of IRE1-mediated unfolded protein response | GO:1903894 | 1 / 3 | 479× | 2.09e-3 | 2.17e-2 ✓ sig. |
| regulation of retrograde transport, endosome to Golgi | GO:1905279 | 1 / 4 | 359× | 2.78e-3 | 2.51e-2 ✓ sig. |
| negative regulation of exosomal secretion | GO:1903542 | 1 / 4 | 359× | 2.78e-3 | 2.51e-2 ✓ sig. |
| dTTP biosynthetic process | GO:0006235 | 1 / 5 | 287× | 3.47e-3 | 2.81e-2 ✓ sig. |
| inner cell mass cell differentiation | GO:0001826 | 1 / 6 | 240× | 4.17e-3 | 3.06e-2 ✓ sig. |
| endodermal cell fate commitment | GO:0001711 | 1 / 6 | 240× | 4.17e-3 | 3.06e-2 ✓ sig. |