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 546
5
Diseases
9
Unique genes
0.224
Avg. similarity score
X-linked sideroblastic anemia
Most-connected disease (4 links)
Disease
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X-linked sideroblastic anemia
Anemia, sideroblastic, 2, pyridoxine-refractory
Erythropoietic protoporphyria
Pyridoxine refractory sideroblastic anemia 2
X-linked erythropoietic protoporphyria
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| X-linked sideroblastic anemia | 4 | 4 | 4 |
| Anemia, sideroblastic, 2, pyridoxine-refractory | 2 | 2 | 1 |
| Erythropoietic protoporphyria | 2 | 2 | 6 |
| Pyridoxine refractory sideroblastic anemia 2 | 2 | 2 | 1 |
| X-linked erythropoietic protoporphyria | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ALAS2 | 3 / 5 | Erythropoietic protoporphyria, X-linked erythropoietic protoporphyria, X-linked sideroblastic anemia |
| SLC25A38 | 3 / 5 | Anemia, sideroblastic, 2, pyridoxine-refractory, Pyridoxine refractory sideroblastic anemia 2, X-linked sideroblastic anemia |
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 ⇵ |
|---|---|---|---|---|---|
| Inhibition of Signaling by Overexpressed EGFR | Reactome | 3 / 8 | 500× | 1.63e-8 | 1.14e-6 ✓ sig. |
| EGFR interacts with phospholipase C-gamma | Reactome | 3 / 9 | 445× | 2.44e-8 | 1.63e-6 ✓ sig. |
| Signaling by EGFR | Reactome | 3 / 11 | 364× | 4.79e-8 | 2.93e-6 ✓ sig. |
| GRB2 events in EGFR signaling | Reactome | 3 / 13 | 308× | 8.29e-8 | 4.73e-6 ✓ sig. |
| SHC1 events in EGFR signaling | Reactome | 3 / 14 | 286× | 1.05e-7 | 5.86e-6 ✓ sig. |
| GAB1 signalosome | Reactome | 3 / 17 | 235× | 1.97e-7 | 1.01e-5 ✓ sig. |
| Estrogen-dependent nuclear events downstream of ESR-membrane signaling | Reactome | 3 / 23 | 174× | 5.12e-7 | 2.33e-5 ✓ sig. |
| EGFR downregulation | Reactome | 3 / 31 | 129× | 1.29e-6 | 5.22e-5 ✓ sig. |
| Extra-nuclear estrogen signaling | Reactome | 3 / 58 | 69.0× | 8.80e-6 | 2.62e-4 ✓ sig. |
| Constitutive Signaling by Aberrant PI3K in Cancer | Reactome | 3 / 75 | 53.4× | 1.91e-5 | 5.02e-4 ✓ sig. |
| PI3K events in ERBB4 signaling | Reactome | 2 / 10 | 267× | 2.24e-5 | 5.72e-4 ✓ sig. |
| Signaling by ERBB4 | Reactome | 2 / 11 | 243× | 2.74e-5 | 6.73e-4 ✓ sig. |
| ErbB signaling pathway | KEGG | 3 / 86 | 46.6× | 2.89e-5 | 7.02e-4 ✓ sig. |
| PIP3 activates AKT signaling | Reactome | 3 / 93 | 43.0× | 3.65e-5 | 8.49e-4 ✓ sig. |
| ERBB2 Activates PTK6 Signaling | Reactome | 2 / 13 | 205× | 3.88e-5 | 8.92e-4 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| ERBB2-EGFR signaling pathway | GO:0038134 | 3 / 8 | 779× | 4.32e-9 | 8.40e-7 ✓ sig. |
| heme biosynthetic process | GO:0006783 | 3 / 27 | 231× | 2.25e-7 | 2.49e-5 ✓ sig. |
| ERBB4-ERBB4 signaling pathway | GO:0038138 | 2 / 6 | 692× | 3.09e-6 | 2.15e-4 ✓ sig. |
| epidermal growth factor receptor signaling pathway | GO:0007173 | 3 / 64 | 97.3× | 3.17e-6 | 2.19e-4 ✓ sig. |
| erythrocyte differentiation | GO:0030218 | 3 / 65 | 95.8× | 3.32e-6 | 2.28e-4 ✓ sig. |
| heme B biosynthetic process | GO:0006785 | 2 / 10 | 415× | 9.26e-6 | 5.13e-4 ✓ sig. |
| positive regulation of phosphorylation | GO:0042327 | 2 / 20 | 208× | 3.90e-5 | 1.53e-3 ✓ sig. |
| positive regulation of mitotic nuclear division | GO:0045840 | 2 / 29 | 143× | 8.32e-5 | 2.70e-3 ✓ sig. |
| positive regulation of cell division | GO:0051781 | 2 / 48 | 86.5× | 2.30e-4 | 5.60e-3 ✓ sig. |
| response to peptide hormone | GO:0043434 | 2 / 50 | 83.1× | 2.50e-4 | 5.94e-3 ✓ sig. |
| positive regulation of fibroblast proliferation | GO:0048146 | 2 / 55 | 75.5× | 3.02e-4 | 6.82e-3 ✓ sig. |
| iron-sulfur cluster export from the mitochondrion | GO:0140466 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| positive regulation of iron-sulfur cluster assembly | GO:1903331 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| glycine import into mitochondrion | GO:1904983 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| detection of UV | GO:0009589 | 1 / 1 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Anemia, sideroblastic, 2, pyridoxine-refractory | Pyridoxine refractory sideroblastic anemia 2 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Anemia, sideroblastic, 2, pyridoxine-refractory | X-linked sideroblastic anemia | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Pyridoxine refractory sideroblastic anemia 2 | X-linked sideroblastic anemia | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| X-linked erythropoietic protoporphyria | X-linked sideroblastic anemia | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Erythropoietic protoporphyria | X-linked erythropoietic protoporphyria | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Erythropoietic protoporphyria | X-linked sideroblastic anemia | 0.100 | 1 | 1.55e-3 | 2.19e-3 ✓ sig. |