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.
← Back to all clusters
Cluster 302
6
Diseases
30
Unique genes
0.139
Avg. similarity score
Skin hair eye pigmentation variation
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) ·
drag a node to pin it in place · scroll/pinch to zoom.
Skin hair eye pigmentation variation
Eye neoplasms
Oculocutaneous albinism
Prader-willi syndrome
Rufous oculocutaneous albinism
Albinism
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Skin hair eye pigmentation variation | 5 | 5 | 7 |
| Eye neoplasms | 3 | 3 | 12 |
| Oculocutaneous albinism | 3 | 3 | 13 |
| Prader-willi syndrome | 2 | 2 | 8 |
| Rufous oculocutaneous albinism | 2 | 2 | 1 |
| Albinism | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| OCA2 | 4 / 6 | Eye neoplasms, Oculocutaneous albinism, Prader-willi syndrome, Skin hair eye pigmentation variation |
| HERC2 | 3 / 6 | Eye neoplasms, Prader-willi syndrome, Skin hair eye pigmentation variation |
| SLC24A5 | 3 / 6 | Eye neoplasms, Oculocutaneous albinism, Skin hair eye pigmentation variation |
| TYRP1 | 3 / 6 | Oculocutaneous albinism, Rufous oculocutaneous albinism, Skin hair eye pigmentation variation |
| SLC45A2 | 2 / 6 | Oculocutaneous albinism, Skin hair eye pigmentation variation |
| TPCN2 | 2 / 6 | Albinism, Skin hair eye pigmentation variation |
| TYR | 2 / 6 | Eye neoplasms, Oculocutaneous albinism |
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 ⇵ |
|---|---|---|---|---|---|
| Melanin biosynthesis | Reactome | 5 / 5 | 400× | 6.85e-14 | 1.81e-11 ✓ sig. |
| Melanogenesis | KEGG | 5 / 101 | 19.8× | 4.59e-6 | 1.77e-4 ✓ sig. |
| Tyrosine metabolism | KEGG | 3 / 36 | 33.4× | 9.50e-5 | 2.15e-3 ✓ sig. |
| Sodium/Calcium exchangers | Reactome | 2 / 13 | 61.6× | 4.63e-4 | 7.50e-3 ✓ sig. |
| Defective SLC24A4 causes hypomineralized amelogenesis imperfecta (AI) | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Defective SLC24A5 causes oculocutaneous albinism 6 (OCA6) | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Defective SLC12A1 causes Bartter syndrome 1 (BS1) | Reactome | 1 / 1 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Neurophilin interactions with VEGF and VEGFR | Reactome | 1 / 4 | 100× | 9.96e-3 | 6.82e-2 |
| Signaling by membrane-tethered fusions of PDGFRA or PDGFRB | Reactome | 1 / 5 | 80.1× | 1.24e-2 | 7.78e-2 |
| Cation-coupled Chloride cotransporters | Reactome | 1 / 7 | 57.2× | 1.74e-2 | 9.50e-2 |
| VEGF binds to VEGFR leading to receptor dimerization | Reactome | 1 / 8 | 50.0× | 1.98e-2 | 1.02e-1 |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 44.5× | 2.23e-2 | 1.09e-1 |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 2 / 108 | 7.4× | 2.96e-2 | 1.28e-1 |
| VEGFR2 mediated cell proliferation | Reactome | 1 / 14 | 28.6× | 3.44e-2 | 1.39e-1 |
| Purine metabolism | KEGG | 2 / 128 | 6.3× | 4.04e-2 | 1.53e-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 ⇵ |
|---|---|---|---|---|---|
| melanin biosynthetic process | GO:0042438 | 7 / 14 | 311× | 4.40e-17 | 4.56e-14 ✓ sig. |
| melanin biosynthetic process from tyrosine | GO:0006583 | 4 / 4 | 623× | 5.40e-12 | 2.11e-9 ✓ sig. |
| pigmentation | GO:0043473 | 6 / 39 | 95.8× | 3.16e-11 | 1.02e-8 ✓ sig. |
| melanocyte differentiation | GO:0030318 | 4 / 21 | 119× | 3.17e-8 | 4.60e-6 ✓ sig. |
| developmental pigmentation | GO:0048066 | 3 / 14 | 133× | 1.34e-6 | 1.05e-4 ✓ sig. |
| response to blue light | GO:0009637 | 2 / 5 | 249× | 2.48e-5 | 1.06e-3 ✓ sig. |
| lysosomal lumen pH elevation | GO:0035752 | 2 / 6 | 208× | 3.72e-5 | 1.44e-3 ✓ sig. |
| sodium ion transmembrane transport | GO:0035725 | 4 / 134 | 18.6× | 5.99e-5 | 2.05e-3 ✓ sig. |
| positive regulation of melanin biosynthetic process | GO:0048023 | 2 / 10 | 125× | 1.11e-4 | 3.27e-3 ✓ sig. |
| transmembrane transport | GO:0055085 | 6 / 557 | 6.7× | 2.20e-4 | 5.40e-3 ✓ sig. |
| response to vitamin D | GO:0033280 | 2 / 21 | 59.3× | 5.13e-4 | 9.72e-3 ✓ sig. |
| melanosome organization | GO:0032438 | 2 / 25 | 49.8× | 7.30e-4 | 1.23e-2 ✓ sig. |
| intracellular calcium ion homeostasis | GO:0006874 | 3 / 113 | 16.5× | 7.76e-4 | 1.28e-2 ✓ sig. |
| negative regulation of cAMP/PKA signal transduction | GO:0141162 | 2 / 28 | 44.5× | 9.18e-4 | 1.43e-2 ✓ sig. |
| protein localization to membrane | GO:0072657 | 2 / 33 | 37.8× | 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 ⇵ |
|---|---|---|---|---|---|
| Oculocutaneous albinism | Skin hair eye pigmentation variation | 0.235 | 4 | 1.07e-11 | 1.24e-10 ✓ sig. |
| Eye neoplasms | Skin hair eye pigmentation variation | 0.176 | 3 | 1.26e-8 | 1.06e-7 ✓ sig. |
| Eye neoplasms | Oculocutaneous albinism | 0.130 | 3 | 1.03e-7 | 7.60e-7 ✓ sig. |
| Prader-willi syndrome | Skin hair eye pigmentation variation | 0.143 | 2 | 4.95e-6 | 2.72e-5 ✓ sig. |
| Eye neoplasms | Prader-willi syndrome | 0.105 | 2 | 1.55e-5 | 7.91e-5 ✓ sig. |
| Albinism | Skin hair eye pigmentation variation | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Rufous oculocutaneous albinism | Skin hair eye pigmentation variation | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Oculocutaneous albinism | Rufous oculocutaneous albinism | 0.071 | 1 | 8.44e-4 | 1.48e-3 ✓ sig. |