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 607
5
Diseases
6
Unique genes
0.306
Avg. similarity score
Facial clefting, oblique, 1
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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Facial clefting, oblique, 1
Opitz gbbb syndrome, type ii
Tessier facial cleft
Commissural facial cleft
Opitz gbbb syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Facial clefting, oblique, 1 | 4 | 4 | 1 |
| Opitz gbbb syndrome, type ii | 4 | 4 | 1 |
| Tessier facial cleft | 4 | 4 | 2 |
| Commissural facial cleft | 3 | 3 | 5 |
| Opitz gbbb syndrome | 3 | 3 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SPECC1L | 5 / 5 | Commissural facial cleft, Facial clefting, oblique, 1, Opitz gbbb syndrome, Opitz gbbb syndrome, type ii and 1 more |
| PTCH2 | 2 / 5 | Commissural facial cleft, Tessier facial cleft |
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 ⇵ |
|---|---|---|---|---|---|
| Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) | Reactome | 1 / 7 | 286× | 3.49e-3 | 2.83e-2 ✓ sig. |
| Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | Reactome | 1 / 14 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| SUMOylation of transcription factors | Reactome | 1 / 18 | 111× | 8.96e-3 | 5.31e-2 |
| Maturity onset diabetes of the young | KEGG | 1 / 26 | 77.0× | 1.29e-2 | 6.62e-2 |
| Pathways in cancer | KEGG | 2 / 533 | 7.5× | 2.62e-2 | 1.00e-1 |
| Hedgehog signaling pathway | KEGG | 1 / 56 | 35.7× | 2.77e-2 | 1.03e-1 |
| Basal cell carcinoma | KEGG | 1 / 63 | 31.8× | 3.11e-2 | 1.10e-1 |
| Melanoma | KEGG | 1 / 73 | 27.4× | 3.59e-2 | 1.20e-1 |
| Interferon gamma signaling | Reactome | 1 / 87 | 23.0× | 4.27e-2 | 1.32e-1 |
| Melanogenesis | KEGG | 1 / 101 | 19.8× | 4.94e-2 | 1.44e-1 |
| Mitophagy - animal | KEGG | 1 / 105 | 19.1× | 5.13e-2 | 1.47e-1 |
| Ubiquitin mediated proteolysis | KEGG | 1 / 142 | 14.1× | 6.89e-2 | 1.74e-1 |
| Osteoclast differentiation | KEGG | 1 / 142 | 14.1× | 6.89e-2 | 1.74e-1 |
| Signaling pathways regulating pluripotency of stem cells | KEGG | 1 / 144 | 13.9× | 6.98e-2 | 1.75e-1 |
| Transcriptional misregulation in cancer | KEGG | 1 / 198 | 10.1× | 9.49e-2 | 2.10e-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 ⇵ |
|---|---|---|---|---|---|
| cell fate determination | GO:0001709 | 2 / 18 | 346× | 1.31e-5 | 6.71e-4 ✓ sig. |
| negative regulation of microtubule depolymerization | GO:0007026 | 2 / 32 | 195× | 4.24e-5 | 1.63e-3 ✓ sig. |
| eye development | GO:0001654 | 2 / 49 | 127× | 1.00e-4 | 3.10e-3 ✓ sig. |
| camera-type eye development | GO:0043010 | 2 / 74 | 84.2× | 2.30e-4 | 5.60e-3 ✓ sig. |
| cell fate commitment | GO:0045165 | 2 / 75 | 83.1× | 2.36e-4 | 5.70e-3 ✓ sig. |
| pancreatic A cell development | GO:0003322 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| forebrain-midbrain boundary formation | GO:0021905 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| neural crest cell delamination | GO:0036032 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| melanocyte apoptotic process | GO:1902362 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| oligodendrocyte cell fate specification | GO:0021778 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| pallium development | GO:0021543 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| habenula development | GO:0021986 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| regulation of RNA biosynthetic process | GO:2001141 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| anterior neural tube closure | GO:0061713 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| regionalization | GO:0003002 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Commissural facial cleft | Tessier facial cleft | 0.333 | 2 | 8.34e-8 | 5.85e-7 ✓ sig. |
| Facial clefting, oblique, 1 | Opitz gbbb syndrome, type ii | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Facial clefting, oblique, 1 | Opitz gbbb syndrome | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Facial clefting, oblique, 1 | Tessier facial cleft | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Opitz gbbb syndrome | Opitz gbbb syndrome, type ii | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Opitz gbbb syndrome, type ii | Tessier facial cleft | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Opitz gbbb syndrome | Tessier facial cleft | 0.250 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Commissural facial cleft | Facial clefting, oblique, 1 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Commissural facial cleft | Opitz gbbb syndrome, type ii | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |