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 376
5
Diseases
11
Unique genes
0.262
Avg. similarity score
Diffuse idiopathic skeletal hyperostosis
Most-connected disease (4 links)
Disease
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Diffuse idiopathic skeletal hyperostosis
PIK3R1-related immunodeficiency and SHORT syndrome
Short syndrome
agammaglobulinemia 7, autosomal recessive
immunodeficiency 122
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Diffuse idiopathic skeletal hyperostosis | 4 | 4 | 11 |
| PIK3R1-related immunodeficiency and SHORT syndrome | 3 | 3 | 1 |
| Short syndrome | 3 | 3 | 1 |
| agammaglobulinemia 7, autosomal recessive | 3 | 3 | 1 |
| immunodeficiency 122 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PIK3R1 | 4 / 5 | agammaglobulinemia 7, autosomal recessive, Diffuse idiopathic skeletal hyperostosis, PIK3R1-related immunodeficiency and SHORT syndrome, Short syndrome |
| POLD3 | 2 / 5 | Diffuse idiopathic skeletal hyperostosis, immunodeficiency 122 |
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 ⇵ |
|---|---|---|---|---|---|
| Zinc efflux and compartmentalization by the SLC30 family | Reactome | 1 / 4 | 273× | 3.66e-3 | 3.54e-2 ✓ sig. |
| Telomere C-strand (Lagging Strand) Synthesis | Reactome | 1 / 5 | 218× | 4.57e-3 | 4.13e-2 ✓ sig. |
| Thyroid hormone signaling pathway | KEGG | 2 / 122 | 17.9× | 5.30e-3 | 4.55e-2 ✓ sig. |
| MET activates PI3K/AKT signaling | Reactome | 1 / 6 | 182× | 5.48e-3 | 4.65e-2 ✓ sig. |
| IRS-mediated signalling | Reactome | 1 / 6 | 182× | 5.48e-3 | 4.65e-2 ✓ sig. |
| Processive synthesis on the C-strand of the telomere | Reactome | 1 / 8 | 136× | 7.31e-3 | 5.62e-2 |
| PI3K/AKT activation | Reactome | 1 / 9 | 121× | 8.22e-3 | 6.07e-2 |
| Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) | Reactome | 1 / 10 | 109× | 9.12e-3 | 6.50e-2 |
| Processive synthesis on the lagging strand | Reactome | 1 / 10 | 109× | 9.12e-3 | 6.50e-2 |
| PI3K events in ERBB4 signaling | Reactome | 1 / 10 | 109× | 9.12e-3 | 6.50e-2 |
| Signaling by FGFR3 fusions in cancer | Reactome | 1 / 10 | 109× | 9.12e-3 | 6.50e-2 |
| JAK-STAT signaling pathway | KEGG | 2 / 168 | 13.0× | 9.85e-3 | 6.80e-2 |
| Removal of the Flap Intermediate from the C-strand | Reactome | 1 / 11 | 99.3× | 1.00e-2 | 6.86e-2 |
| Signaling by FGFR4 in disease | Reactome | 1 / 11 | 99.3× | 1.00e-2 | 6.86e-2 |
| Costimulation by the CD28 family | Reactome | 1 / 11 | 99.3× | 1.00e-2 | 6.86e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| transcription by RNA polymerase II | GO:0006366 | 3 / 261 | 19.5× | 4.09e-4 | 8.35e-3 ✓ sig. |
| B cell differentiation | GO:0030183 | 2 / 80 | 42.5× | 9.71e-4 | 1.47e-2 ✓ sig. |
| positive regulation of endoplasmic reticulum unfolded protein response | GO:1900103 | 1 / 2 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| DNA synthesis involved in UV-damage excision repair | GO:1904161 | 1 / 3 | 566× | 1.76e-3 | 2.11e-2 ✓ sig. |
| myeloid leukocyte migration | GO:0097529 | 1 / 4 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| nucleotide-excision repair, DNA gap filling | GO:0006297 | 1 / 6 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| interleukin-11-mediated signaling pathway | GO:0038154 | 1 / 7 | 243× | 4.11e-3 | 3.32e-2 ✓ sig. |
| regulation of toll-like receptor 4 signaling pathway | GO:0034143 | 1 / 7 | 243× | 4.11e-3 | 3.32e-2 ✓ sig. |
| zinc ion import into organelle | GO:0062111 | 1 / 7 | 243× | 4.11e-3 | 3.32e-2 ✓ sig. |
| regulation of complement-dependent cytotoxicity | GO:1903659 | 1 / 8 | 212× | 4.70e-3 | 3.56e-2 ✓ sig. |
| positive regulation of focal adhesion disassembly | GO:0120183 | 1 / 8 | 212× | 4.70e-3 | 3.56e-2 ✓ sig. |
| DNA strand elongation involved in DNA replication | GO:0006271 | 1 / 8 | 212× | 4.70e-3 | 3.56e-2 ✓ sig. |
| insulin processing | GO:0030070 | 1 / 9 | 189× | 5.29e-3 | 3.78e-2 ✓ sig. |
| zinc ion import across plasma membrane | GO:0071578 | 1 / 10 | 170× | 5.87e-3 | 3.98e-2 ✓ sig. |
| negative regulation of hormone secretion | GO:0046888 | 1 / 10 | 170× | 5.87e-3 | 3.98e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| agammaglobulinemia 7, autosomal recessive | Short syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| agammaglobulinemia 7, autosomal recessive | PIK3R1-related immunodeficiency and SHORT syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| PIK3R1-related immunodeficiency and SHORT syndrome | Short syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| agammaglobulinemia 7, autosomal recessive | Diffuse idiopathic skeletal hyperostosis | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Diffuse idiopathic skeletal hyperostosis | Short syndrome | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Diffuse idiopathic skeletal hyperostosis | PIK3R1-related immunodeficiency and SHORT syndrome | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |
| Diffuse idiopathic skeletal hyperostosis | immunodeficiency 122 | 0.083 | 1 | 7.14e-4 | 1.31e-3 ✓ sig. |