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 311
6
Diseases
5
Unique genes
0.283
Avg. similarity score
Micropenis
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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Micropenis
Yunis-varon syndrome
Bilateral parasagittal parieto-occipital polymicrogyria
amyotrophic lateral sclerosis type 11
Childhood-onset basal ganglia degeneration syndrome
hypogonadotropic hypogonadism 1 with or without anosmia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Micropenis | 4 | 4 | 4 |
| Yunis-varon syndrome | 4 | 4 | 2 |
| Bilateral parasagittal parieto-occipital polymicrogyria | 3 | 3 | 1 |
| amyotrophic lateral sclerosis type 11 | 3 | 3 | 1 |
| Childhood-onset basal ganglia degeneration syndrome | 1 | 1 | 1 |
| hypogonadotropic hypogonadism 1 with or without anosmia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FIG4 | 4 / 6 | amyotrophic lateral sclerosis type 11, Bilateral parasagittal parieto-occipital polymicrogyria, Micropenis, Yunis-varon syndrome |
| ANOS1 | 2 / 6 | hypogonadotropic hypogonadism 1 with or without anosmia, Micropenis |
| VAC14 | 2 / 6 | Childhood-onset basal ganglia degeneration syndrome, Yunis-varon 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 ⇵ |
|---|---|---|---|---|---|
| Synthesis of PIPs at the late endosome membrane | Reactome | 2 / 10 | 480× | 6.23e-6 | 2.26e-4 ✓ sig. |
| Synthesis of PIPs at the early endosome membrane | Reactome | 2 / 15 | 320× | 1.45e-5 | 4.57e-4 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 2 / 18 | 267× | 2.12e-5 | 6.27e-4 ✓ sig. |
| Androgen biosynthesis | Reactome | 1 / 11 | 218× | 4.57e-3 | 4.13e-2 ✓ sig. |
| FGFR1c ligand binding and activation | Reactome | 1 / 12 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| BBSome-mediated cargo-targeting to cilium | Reactome | 1 / 23 | 104× | 9.54e-3 | 6.67e-2 |
| Negative regulation of FGFR1 signaling | Reactome | 1 / 26 | 92.4× | 1.08e-2 | 7.19e-2 |
| Steroid hormone biosynthesis | KEGG | 1 / 63 | 38.1× | 2.60e-2 | 1.19e-1 |
| Inositol phosphate metabolism | KEGG | 1 / 73 | 32.9× | 3.00e-2 | 1.29e-1 |
| Prostate cancer | KEGG | 1 / 98 | 24.5× | 4.01e-2 | 1.52e-1 |
| Viral carcinogenesis | KEGG | 1 / 205 | 11.7× | 8.25e-2 | 2.23e-1 |
| Human T-cell leukemia virus 1 infection | KEGG | 1 / 224 | 10.7× | 8.99e-2 | 2.33e-1 |
| Metabolic pathways | KEGG | 2 / 1,563 | 3.1× | 1.29e-1 | 2.85e-1 |
| Amyotrophic lateral sclerosis | KEGG | 1 / 368 | 6.5× | 1.44e-1 | 3.03e-1 |
| Pathways of neurodegeneration - multiple diseases | KEGG | 1 / 480 | 5.0× | 1.85e-1 | 3.48e-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 ⇵ |
|---|---|---|---|---|---|
| phosphatidylinositol biosynthetic process | GO:0006661 | 2 / 44 | 170× | 5.39e-5 | 1.90e-3 ✓ sig. |
| phthalate metabolic process | GO:0018963 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| biphenyl metabolic process | GO:0018879 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| dibenzo-p-dioxin metabolic process | GO:0018894 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| response to biphenyl | GO:1904614 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| response to follicle-stimulating hormone | GO:0032354 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| receptor localization to non-motile cilium | GO:0097500 | 1 / 5 | 747× | 1.34e-3 | 1.79e-2 ✓ sig. |
| testosterone biosynthetic process | GO:0061370 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| steroid catabolic process | GO:0006706 | 1 / 7 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| myelin assembly | GO:0032288 | 1 / 7 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| female genitalia development | GO:0030540 | 1 / 7 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| androgen biosynthetic process | GO:0006702 | 1 / 9 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| negative regulation of myelination | GO:0031642 | 1 / 9 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| leukocyte homeostasis | GO:0001776 | 1 / 9 | 415× | 2.41e-3 | 2.50e-2 ✓ sig. |
| myeloid cell homeostasis | GO:0002262 | 1 / 11 | 340× | 2.94e-3 | 2.79e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| amyotrophic lateral sclerosis type 11 | Bilateral parasagittal parieto-occipital polymicrogyria | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| amyotrophic lateral sclerosis type 11 | Yunis-varon syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Bilateral parasagittal parieto-occipital polymicrogyria | Yunis-varon syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Childhood-onset basal ganglia degeneration syndrome | Yunis-varon syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| amyotrophic lateral sclerosis type 11 | Micropenis | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Bilateral parasagittal parieto-occipital polymicrogyria | Micropenis | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| hypogonadotropic hypogonadism 1 with or without anosmia | Micropenis | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Micropenis | Yunis-varon syndrome | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |