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 283
6
Diseases
7
Unique genes
0.299
Avg. similarity score
Tietz syndrome
Most-connected disease (5 links)
Disease
Searched: qualitative platelet defect
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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qualitative platelet defect
Tietz syndrome
12q14 microdeletion syndrome
Buschke-ollendorff syndrome
Dermatofibrosis lenticularis disseminata
Osteopoikilosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Tietz syndrome | 5 | 5 | 5 |
| 12q14 microdeletion syndrome | 4 | 4 | 2 |
| Buschke-ollendorff syndrome | 4 | 4 | 1 |
| Dermatofibrosis lenticularis disseminata | 4 | 4 | 1 |
| Osteopoikilosis | 4 | 4 | 1 |
| qualitative platelet defect | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LEMD3 | 5 / 6 | 12q14 microdeletion syndrome, Buschke-ollendorff syndrome, Dermatofibrosis lenticularis disseminata, Osteopoikilosis and 1 more |
| ABCC4 | 2 / 6 | qualitative platelet defect, Tietz 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)
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Conjugation of benzoate with glycine | Reactome | 1 / 6 | 286× | 3.49e-3 | 3.48e-2 ✓ sig. |
| Conjugation of salicylate with glycine | Reactome | 1 / 8 | 214× | 4.65e-3 | 4.24e-2 ✓ sig. |
| Prostanoid ligand receptors | Reactome | 1 / 9 | 191× | 5.24e-3 | 4.60e-2 ✓ sig. |
| Nuclear Envelope Breakdown | Reactome | 1 / 9 | 191× | 5.24e-3 | 4.60e-2 ✓ sig. |
| Transcriptional misregulation in cancer | KEGG | 2 / 198 | 17.3× | 5.38e-3 | 4.69e-2 ✓ sig. |
| Depolymerisation of the Nuclear Lamina | Reactome | 1 / 15 | 114× | 8.71e-3 | 6.44e-2 |
| Calcium signaling pathway | KEGG | 2 / 254 | 13.5× | 8.72e-3 | 6.44e-2 |
| Formation of Senescence-Associated Heterochromatin Foci (SAHF) | Reactome | 1 / 16 | 107× | 9.29e-3 | 6.69e-2 |
| SUMOylation of transcription factors | Reactome | 1 / 18 | 95.3× | 1.04e-2 | 7.20e-2 |
| Initiation of Nuclear Envelope (NE) Reformation | Reactome | 1 / 19 | 90.3× | 1.10e-2 | 7.44e-2 |
| Thromboxane signalling through TP receptor | Reactome | 1 / 24 | 71.5× | 1.39e-2 | 8.55e-2 |
| Antifolate resistance | KEGG | 1 / 30 | 57.2× | 1.74e-2 | 9.78e-2 |
| Folate transport and metabolism | KEGG | 1 / 31 | 55.3× | 1.79e-2 | 9.98e-2 |
| ABC transporters | KEGG | 1 / 45 | 38.1× | 2.59e-2 | 1.23e-1 |
| Melanoma | KEGG | 1 / 73 | 23.5× | 4.18e-2 | 1.58e-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 ⇵ |
|---|---|---|---|---|---|
| mesodermal-endodermal cell signaling | GO:0003131 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| thromboxane A2 signaling pathway | GO:0038193 | 1 / 1 | 2,670× | 3.75e-4 | 8.02e-3 ✓ sig. |
| cAMP transport | GO:0070730 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| guanine nucleotide transmembrane transport | GO:1903790 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| melanocyte apoptotic process | GO:1902362 | 1 / 2 | 1,335× | 7.49e-4 | 1.28e-2 ✓ sig. |
| regulation of growth hormone secretion | GO:0060123 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| regulation of peptide hormone secretion | GO:0090276 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| regulation of RNA biosynthetic process | GO:2001141 | 1 / 3 | 890× | 1.12e-3 | 1.66e-2 ✓ sig. |
| positive regulation of angiogenesis | GO:0045766 | 2 / 159 | 33.6× | 1.47e-3 | 1.93e-2 ✓ sig. |
| negative regulation of intracellular steroid hormone receptor signaling pathway | GO:0033144 | 1 / 4 | 667× | 1.50e-3 | 1.95e-2 ✓ sig. |
| positive regulation of cell proliferation in bone marrow | GO:0071864 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| platelet degranulation | GO:0002576 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| prostaglandin secretion | GO:0032310 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| activation of store-operated calcium channel activity | GO:0032237 | 1 / 5 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| positive regulation of epithelial cell proliferation involved in lung morphogenesis | GO:0060501 | 1 / 7 | 381× | 2.62e-3 | 2.70e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Buschke-ollendorff syndrome | Dermatofibrosis lenticularis disseminata | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Buschke-ollendorff syndrome | Osteopoikilosis | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| Dermatofibrosis lenticularis disseminata | Osteopoikilosis | 0.500 | 1 | 6.49e-5 | 2.32e-4 ✓ sig. |
| 12q14 microdeletion syndrome | Buschke-ollendorff syndrome | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| 12q14 microdeletion syndrome | Dermatofibrosis lenticularis disseminata | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| 12q14 microdeletion syndrome | Osteopoikilosis | 0.333 | 1 | 1.30e-4 | 3.91e-4 ✓ sig. |
| Buschke-ollendorff syndrome | Tietz syndrome | 0.167 | 1 | 3.25e-4 | 7.68e-4 ✓ sig. |
| Dermatofibrosis lenticularis disseminata | Tietz syndrome | 0.167 | 1 | 3.25e-4 | 7.68e-4 ✓ sig. |
| Osteopoikilosis | Tietz syndrome | 0.167 | 1 | 3.25e-4 | 7.68e-4 ✓ sig. |
| qualitative platelet defect | Tietz syndrome | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |
| 12q14 microdeletion syndrome | Tietz syndrome | 0.143 | 1 | 6.49e-4 | 1.24e-3 ✓ sig. |