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 418
5
Diseases
5
Unique genes
0.297
Avg. similarity score
Congenital fusion of ribs
Most-connected disease (3 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Congenital fusion of ribs
Borjeson-forssman-lehmann syndrome
Congenital hypoplasia of penis
Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome
Cerebrofaciothoracic dysplasia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital fusion of ribs | 3 | 3 | 4 |
| Borjeson-forssman-lehmann syndrome | 2 | 2 | 1 |
| Congenital hypoplasia of penis | 2 | 2 | 1 |
| Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome | 2 | 2 | 3 |
| Cerebrofaciothoracic dysplasia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PHF6 | 3 / 5 | Borjeson-forssman-lehmann syndrome, Congenital fusion of ribs, Congenital hypoplasia of penis |
| RAB5IF | 2 / 5 | Congenital fusion of ribs, Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome |
| TGIF2-RAB5IF | 2 / 5 | Congenital fusion of ribs, Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome |
| TMCO1 | 2 / 5 | Cerebrofaciothoracic dysplasia, Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome |
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)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Notch signaling pathway | KEGG | 1 / 62 | 38.7× | 2.56e-2 | 1.18e-1 |
| Th1 and Th2 cell differentiation | KEGG | 1 / 93 | 25.8× | 3.81e-2 | 1.48e-1 |
| Endocrine resistance | KEGG | 1 / 99 | 24.3× | 4.05e-2 | 1.53e-1 |
| ATP-dependent chromatin remodeling | KEGG | 1 / 117 | 20.5× | 4.78e-2 | 1.67e-1 |
| Breast cancer | KEGG | 1 / 148 | 16.2× | 6.01e-2 | 1.89e-1 |
| Chemical carcinogenesis - receptor activation | KEGG | 1 / 215 | 11.2× | 8.64e-2 | 2.29e-1 |
| Pathways in cancer | KEGG | 1 / 533 | 4.5× | 2.03e-1 | 3.67e-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 ⇵ |
|---|---|---|---|---|---|
| multi-pass transmembrane protein insertion into ER membrane | GO:0160063 | 2 / 9 | 831× | 2.06e-6 | 1.47e-4 ✓ sig. |
| compartment pattern specification | GO:0007386 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| ER overload response | GO:0006983 | 1 / 11 | 340× | 2.94e-3 | 2.79e-2 ✓ sig. |
| paraxial mesoderm development | GO:0048339 | 1 / 11 | 340× | 2.94e-3 | 2.79e-2 ✓ sig. |
| mitochondrial respirasome assembly | GO:0097250 | 1 / 12 | 311× | 3.21e-3 | 2.91e-2 ✓ sig. |
| endoplasmic reticulum calcium ion homeostasis | GO:0032469 | 1 / 19 | 197× | 5.07e-3 | 3.71e-2 ✓ sig. |
| blastocyst hatching | GO:0001835 | 1 / 30 | 125× | 8.00e-3 | 4.60e-2 ✓ sig. |
| negative regulation of neurogenesis | GO:0050768 | 1 / 30 | 125× | 8.00e-3 | 4.60e-2 ✓ sig. |
| negative regulation of Notch signaling pathway | GO:0045746 | 1 / 42 | 89.0× | 1.12e-2 | 5.41e-2 |
| somitogenesis | GO:0001756 | 1 / 50 | 74.7× | 1.33e-2 | 5.90e-2 |
| tissue development | GO:0009888 | 1 / 51 | 73.3× | 1.36e-2 | 5.95e-2 |
| ossification | GO:0001503 | 1 / 110 | 34.0× | 2.91e-2 | 8.64e-2 |
| Notch signaling pathway | GO:0007219 | 1 / 117 | 31.9× | 3.09e-2 | 8.93e-2 |
| calcium ion transmembrane transport | GO:0070588 | 1 / 149 | 25.1× | 3.92e-2 | 1.01e-1 |
| skeletal system development | GO:0001501 | 1 / 151 | 24.8× | 3.98e-2 | 1.02e-1 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital fusion of ribs | Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome | 0.333 | 2 | 1.52e-7 | 1.09e-6 ✓ sig. |
| Borjeson-forssman-lehmann syndrome | Congenital hypoplasia of penis | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Cerebrofaciothoracic dysplasia | Craniofacial dysmorphism skeletal anomalies intellectual disability syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Borjeson-forssman-lehmann syndrome | Congenital fusion of ribs | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Congenital fusion of ribs | Congenital hypoplasia of penis | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |