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 263
7
Diseases
5
Unique genes
0.300
Avg. similarity score
Congenital camptodactyly
Most-connected disease (5 links)
Disease
Searched: Congenital camptodactyly
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Congenital camptodactyly
Bowed long bones
Buruli ulcer
Congenital hypoplasia of femur
Cardiac anomalies - developmental delay - facial dysmorphism syndrome
Developmental delay with facial dysmorphism syndrome
asphyxiating thoracic dystrophy 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital camptodactyly | 5 | 5 | 2 |
| Bowed long bones | 4 | 4 | 2 |
| Buruli ulcer | 3 | 3 | 2 |
| Congenital hypoplasia of femur | 3 | 3 | 2 |
| Cardiac anomalies - developmental delay - facial dysmorphism syndrome | 2 | 2 | 1 |
| Developmental delay with facial dysmorphism syndrome | 2 | 2 | 1 |
| asphyxiating thoracic dystrophy 3 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PLOD2 | 4 / 7 | Bowed long bones, Buruli ulcer, Congenital camptodactyly, Congenital hypoplasia of femur |
| MED13L | 3 / 7 | Cardiac anomalies - developmental delay - facial dysmorphism syndrome, Congenital camptodactyly, Developmental delay with facial dysmorphism syndrome |
| DYNC2H1 | 2 / 7 | asphyxiating thoracic dystrophy 3, Bowed long bones |
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 ⇵ |
|---|---|---|---|---|---|
| ARL13B-mediated ciliary trafficking of INPP5E | Reactome | 1 / 3 | 801× | 1.25e-3 | 1.66e-2 ✓ sig. |
| Ion influx/efflux at host-pathogen interface | Reactome | 1 / 4 | 601× | 1.66e-3 | 2.07e-2 ✓ sig. |
| Metal ion SLC transporters | Reactome | 1 / 9 | 267× | 3.74e-3 | 3.69e-2 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 1 / 18 | 133× | 7.47e-3 | 5.89e-2 |
| ROS and RNS production in phagocytes | Reactome | 1 / 34 | 70.6× | 1.41e-2 | 8.70e-2 |
| Vasopressin-regulated water reabsorption | KEGG | 1 / 44 | 54.6× | 1.82e-2 | 1.02e-1 |
| Intraflagellar transport | Reactome | 1 / 54 | 44.5× | 2.23e-2 | 1.14e-1 |
| Hedgehog 'off' state | Reactome | 1 / 56 | 42.9× | 2.31e-2 | 1.16e-1 |
| Lysine degradation | KEGG | 1 / 63 | 38.1× | 2.60e-2 | 1.24e-1 |
| Transcriptional regulation of white adipocyte differentiation | Reactome | 1 / 67 | 35.9× | 2.76e-2 | 1.28e-1 |
| Collagen biosynthesis and modifying enzymes | Reactome | 1 / 67 | 35.9× | 2.76e-2 | 1.28e-1 |
| Inositol phosphate metabolism | KEGG | 1 / 73 | 32.9× | 3.00e-2 | 1.34e-1 |
| Phosphatidylinositol signaling system | KEGG | 1 / 98 | 24.5× | 4.01e-2 | 1.57e-1 |
| PPARA activates gene expression | Reactome | 1 / 115 | 20.9× | 4.70e-2 | 1.70e-1 |
| Thyroid hormone signaling pathway | KEGG | 1 / 122 | 19.7× | 4.98e-2 | 1.76e-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 ⇵ |
|---|---|---|---|---|---|
| nitrite transport | GO:0015707 | 1 / 1 | 3,737× | 2.68e-4 | 6.41e-3 ✓ sig. |
| hydroxylysine biosynthetic process | GO:0046947 | 1 / 2 | 1,869× | 5.35e-4 | 1.03e-2 ✓ sig. |
| MHC class II biosynthetic process | GO:0045342 | 1 / 2 | 1,869× | 5.35e-4 | 1.03e-2 ✓ sig. |
| cellular detoxification of cadmium ion | GO:0098849 | 1 / 3 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| antigen processing and presentation of peptide antigen | GO:0048002 | 1 / 3 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| negative regulation of protein localization to cilium | GO:1903565 | 1 / 3 | 1,246× | 8.03e-4 | 1.35e-2 ✓ sig. |
| response to inositol | GO:1902140 | 1 / 4 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| T cell proliferation involved in immune response | GO:0002309 | 1 / 4 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| intracellular manganese ion homeostasis | GO:0030026 | 1 / 5 | 747× | 1.34e-3 | 1.86e-2 ✓ sig. |
| cilium assembly | GO:0060271 | 2 / 237 | 31.5× | 1.56e-3 | 2.04e-2 ✓ sig. |
| cadmium ion transmembrane transport | GO:0070574 | 1 / 6 | 623× | 1.60e-3 | 2.06e-2 ✓ sig. |
| positive regulation of dendritic cell antigen processing and presentation | GO:0002606 | 1 / 7 | 534× | 1.87e-3 | 2.26e-2 ✓ sig. |
| peptidyl-lysine hydroxylation | GO:0017185 | 1 / 7 | 534× | 1.87e-3 | 2.26e-2 ✓ sig. |
| organophosphate metabolic process | GO:0019637 | 1 / 8 | 467× | 2.14e-3 | 2.42e-2 ✓ sig. |
| manganese ion transport | GO:0006828 | 1 / 9 | 415× | 2.41e-3 | 2.59e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cardiac anomalies - developmental delay - facial dysmorphism syndrome | Developmental delay with facial dysmorphism syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| asphyxiating thoracic dystrophy 3 | Bowed long bones | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Cardiac anomalies - developmental delay - facial dysmorphism syndrome | Congenital camptodactyly | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Congenital camptodactyly | Developmental delay with facial dysmorphism syndrome | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Bowed long bones | Buruli ulcer | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Bowed long bones | Congenital camptodactyly | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Bowed long bones | Congenital hypoplasia of femur | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Buruli ulcer | Congenital camptodactyly | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Buruli ulcer | Congenital hypoplasia of femur | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Congenital camptodactyly | Congenital hypoplasia of femur | 0.250 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |