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 317
6
Diseases
6
Unique genes
0.265
Avg. similarity score
Anisometropia
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Anisometropia
Lipomatosis
Concussion
PTEN hamartoma tumor syndrome
Trichiasis
maturity-onset diabetes of the young type 8
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Anisometropia | 4 | 4 | 2 |
| Lipomatosis | 4 | 4 | 2 |
| Concussion | 3 | 3 | 4 |
| PTEN hamartoma tumor syndrome | 3 | 3 | 1 |
| Trichiasis | 1 | 1 | 1 |
| maturity-onset diabetes of the young type 8 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PTEN | 4 / 6 | Anisometropia, Concussion, Lipomatosis, PTEN hamartoma tumor syndrome |
| CEL | 2 / 6 | Lipomatosis, maturity-onset diabetes of the young type 8 |
| MCM7 | 2 / 6 | Anisometropia, Trichiasis |
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 ⇵ |
|---|---|---|---|---|---|
| PTEN Loss of Function in Cancer | Reactome | 1 / 1 | 2,002× | 5.00e-4 | 7.96e-3 ✓ sig. |
| Switching of origins to a post-replicative state | Reactome | 1 / 6 | 334× | 2.99e-3 | 3.07e-2 ✓ sig. |
| Negative regulation of the PI3K/AKT network | Reactome | 1 / 8 | 250× | 3.99e-3 | 3.77e-2 ✓ sig. |
| Regulation of PTEN mRNA translation | Reactome | 1 / 9 | 222× | 4.49e-3 | 4.08e-2 ✓ sig. |
| Regulation of PTEN localization | Reactome | 1 / 9 | 222× | 4.49e-3 | 4.08e-2 ✓ sig. |
| SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion | Reactome | 1 / 10 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Transcriptional Regulation by MECP2 | Reactome | 1 / 10 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Triglyceride biosynthesis | Reactome | 1 / 13 | 154× | 6.48e-3 | 5.19e-2 |
| Sema3A PAK dependent Axon repulsion | Reactome | 1 / 15 | 133× | 7.47e-3 | 5.69e-2 |
| Assembly of the pre-replicative complex | Reactome | 1 / 15 | 133× | 7.47e-3 | 5.69e-2 |
| CRMPs in Sema3A signaling | Reactome | 1 / 16 | 125× | 7.97e-3 | 5.96e-2 |
| Steroid biosynthesis | KEGG | 1 / 20 | 100× | 9.95e-3 | 6.82e-2 |
| Synthesis of IP3 and IP4 in the cytosol | Reactome | 1 / 28 | 71.5× | 1.39e-2 | 8.31e-2 |
| Activation of the pre-replicative complex | Reactome | 1 / 33 | 60.7× | 1.64e-2 | 9.17e-2 |
| DNA replication | KEGG | 1 / 36 | 55.6× | 1.79e-2 | 9.67e-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 ⇵ |
|---|---|---|---|---|---|
| synapse assembly | GO:0007416 | 2 / 78 | 79.9× | 2.55e-4 | 5.99e-3 ✓ sig. |
| negative regulation of cell communication | GO:0010648 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| negative regulation of synaptic vesicle clustering | GO:2000808 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| chemorepulsion of branchiomotor axon | GO:0021793 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| regulation of negative chemotaxis | GO:0050923 | 1 / 1 | 3,115× | 3.21e-4 | 7.03e-3 ✓ sig. |
| trigeminal nerve morphogenesis | GO:0021636 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| negative regulation of keratinocyte migration | GO:0051548 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| postganglionic parasympathetic fiber development | GO:0021784 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| cranial nerve morphogenesis | GO:0021602 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| vagus nerve morphogenesis | GO:0021644 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| membrane lipid metabolic process | GO:0006643 | 1 / 2 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| facial nerve morphogenesis | GO:0021610 | 1 / 3 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| negative regulation of signaling | GO:0023057 | 1 / 3 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| rhythmic synaptic transmission | GO:0060024 | 1 / 3 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| regulation of axon extension involved in axon guidance | GO:0048841 | 1 / 4 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Anisometropia | PTEN hamartoma tumor syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Anisometropia | Trichiasis | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Lipomatosis | PTEN hamartoma tumor syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Lipomatosis | maturity-onset diabetes of the young type 8 | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Anisometropia | Lipomatosis | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Concussion | PTEN hamartoma tumor syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Anisometropia | Concussion | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |
| Concussion | Lipomatosis | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |