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 358
5
Diseases
4
Unique genes
0.345
Avg. similarity score
Partial agenesis of corpus callosum
Most-connected disease (4 links)
Disease
Searched: holoprosencephaly 3
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holoprosencephaly 3
Partial agenesis of corpus callosum
Preaxial polydactyly with upper back hypertrichosis
Skeletal system disorder
Triphalangeal thumb-polysyndactyly syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Partial agenesis of corpus callosum | 4 | 4 | 3 |
| Preaxial polydactyly with upper back hypertrichosis | 4 | 4 | 1 |
| Skeletal system disorder | 4 | 4 | 1 |
| Triphalangeal thumb-polysyndactyly syndrome | 4 | 4 | 2 |
| holoprosencephaly 3 | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SHH | 5 / 5 | holoprosencephaly 3, Partial agenesis of corpus callosum, Preaxial polydactyly with upper back hypertrichosis, Skeletal system disorder and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Caspase activation via Dependence Receptors in the absence of ligand | Reactome | 1 / 4 | 751× | 1.33e-3 | 1.73e-2 ✓ sig. |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 751× | 1.33e-3 | 1.73e-2 ✓ sig. |
| Axon guidance | KEGG | 2 / 183 | 32.8× | 1.36e-3 | 1.75e-2 ✓ sig. |
| Release of Hh-Np from the secreting cell | Reactome | 1 / 7 | 429× | 2.33e-3 | 2.61e-2 ✓ sig. |
| Ligand-receptor interactions | Reactome | 1 / 7 | 429× | 2.33e-3 | 2.61e-2 ✓ sig. |
| Netrin-1 signaling | Reactome | 1 / 8 | 375× | 2.66e-3 | 2.88e-2 ✓ sig. |
| DCC mediated attractive signaling | Reactome | 1 / 11 | 273× | 3.66e-3 | 3.60e-2 ✓ sig. |
| Activation of SMO | Reactome | 1 / 18 | 167× | 5.98e-3 | 5.03e-2 |
| Pathways in cancer | KEGG | 2 / 533 | 11.3× | 1.11e-2 | 7.48e-2 |
| Basal transcription factors | KEGG | 1 / 44 | 68.2× | 1.46e-2 | 8.79e-2 |
| Hedgehog signaling pathway | KEGG | 1 / 56 | 53.6× | 1.85e-2 | 1.02e-1 |
| Hh mutants that don't undergo autocatalytic processing are degraded by ERAD | Reactome | 1 / 56 | 53.6× | 1.85e-2 | 1.02e-1 |
| Hedgehog ligand biogenesis | Reactome | 1 / 60 | 50.0× | 1.98e-2 | 1.05e-1 |
| Basal cell carcinoma | KEGG | 1 / 63 | 47.7× | 2.08e-2 | 1.08e-1 |
| RNA polymerase II transcribes snRNA genes | Reactome | 1 / 74 | 40.6× | 2.44e-2 | 1.19e-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 ⇵ |
|---|---|---|---|---|---|
| embryonic digit morphogenesis | GO:0042733 | 2 / 57 | 164× | 5.46e-5 | 1.96e-3 ✓ sig. |
| polarity specification of anterior/posterior axis | GO:0009949 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| cell proliferation in external granule layer | GO:0021924 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| right lung development | GO:0060458 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| left lung development | GO:0060459 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| primary prostatic bud elongation | GO:0060516 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| epithelial-mesenchymal signaling involved in prostate gland development | GO:0060738 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| regulation of mesenchymal cell proliferation involved in prostate gland development | GO:0060782 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| mesenchymal smoothened signaling pathway involved in prostate gland development | GO:0060783 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| positive regulation of sclerotome development | GO:0061189 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| tracheoesophageal septum formation | GO:1905327 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| negative regulation of ureter smooth muscle cell differentiation | GO:2000062 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| positive regulation of ureter smooth muscle cell differentiation | GO:2000063 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| negative regulation of kidney smooth muscle cell differentiation | GO:2000357 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |
| positive regulation of kidney smooth muscle cell differentiation | GO:2000358 | 1 / 1 | 4,672× | 2.14e-4 | 5.39e-3 ✓ sig. |