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 103
11
Diseases
36
Unique genes
0.193
Avg. similarity score
Penile hypospadia
Most-connected disease (6 links)
Disease
Searched: hypogonadotropic hypogonadism 1 with or without anosmia
Pinned (dragged)
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hypogonadotropic hypogonadism 1 with or without anosmia
Penile hypospadia
Yunis-varon syndrome
Bilateral parasagittal parieto-occipital polymicrogyria
Micropenis
amyotrophic lateral sclerosis type 11
Cryptorchidism
Ghosal hematodiaphyseal dysplasia
Imperforate anus
Biotinidase deficiency
Childhood-onset basal ganglia degeneration syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Penile hypospadia | 6 | 6 | 8 |
| Yunis-varon syndrome | 5 | 5 | 2 |
| Bilateral parasagittal parieto-occipital polymicrogyria | 4 | 4 | 1 |
| Micropenis | 4 | 4 | 4 |
| amyotrophic lateral sclerosis type 11 | 4 | 4 | 1 |
| Cryptorchidism | 2 | 2 | 20 |
| Ghosal hematodiaphyseal dysplasia | 2 | 2 | 1 |
| Imperforate anus | 2 | 2 | 9 |
| Biotinidase deficiency | 1 | 1 | 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 | 5 / 11 | amyotrophic lateral sclerosis type 11, Bilateral parasagittal parieto-occipital polymicrogyria, Micropenis, Penile hypospadia and 1 more |
| TBXAS1 | 3 / 11 | Ghosal hematodiaphyseal dysplasia, Imperforate anus, Penile hypospadia |
| ANOS1 | 2 / 11 | hypogonadotropic hypogonadism 1 with or without anosmia, Micropenis |
| BTD | 2 / 11 | Biotinidase deficiency, Cryptorchidism |
| GABRG3 | 2 / 11 | Imperforate anus, Penile hypospadia |
| HOXD13 | 2 / 11 | Cryptorchidism, Penile hypospadia |
| LSM1 | 2 / 11 | Cryptorchidism, Penile hypospadia |
| NIPBL | 2 / 11 | Cryptorchidism, Penile hypospadia |
| VAC14 | 2 / 11 | 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 ⇵ |
|---|---|---|---|---|---|
| Relaxin receptors | Reactome | 2 / 8 | 83.4× | 2.42e-4 | 4.65e-3 ✓ sig. |
| Synthesis of PIPs at the late endosome membrane | Reactome | 2 / 10 | 66.7× | 3.87e-4 | 6.77e-3 ✓ sig. |
| Apoptotic cleavage of cell adhesion proteins | Reactome | 2 / 11 | 60.7× | 4.72e-4 | 7.94e-3 ✓ sig. |
| Androgen biosynthesis | Reactome | 2 / 11 | 60.7× | 4.72e-4 | 7.94e-3 ✓ sig. |
| Synthesis of PIPs at the early endosome membrane | Reactome | 2 / 15 | 44.5× | 8.95e-4 | 1.29e-2 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 2 / 18 | 37.1× | 1.30e-3 | 1.71e-2 ✓ sig. |
| Negative regulation of FGFR1 signaling | Reactome | 2 / 26 | 25.7× | 2.71e-3 | 2.95e-2 ✓ sig. |
| Pathways of neurodegeneration - multiple diseases | KEGG | 6 / 480 | 4.2× | 2.77e-3 | 2.99e-2 ✓ sig. |
| Defective BTD causes biotidinase deficiency | Reactome | 1 / 1 | 334× | 3.00e-3 | 3.15e-2 ✓ sig. |
| Defective TBXAS1 causes Ghosal hematodiaphyseal dysplasia (GHDD) | Reactome | 1 / 1 | 334× | 3.00e-3 | 3.15e-2 ✓ sig. |
| Prostate cancer | KEGG | 3 / 98 | 10.2× | 3.09e-3 | 3.22e-2 ✓ sig. |
| Apoptosis - multiple species | KEGG | 2 / 32 | 20.9× | 4.09e-3 | 3.94e-2 ✓ sig. |
| RHO GTPases activate IQGAPs | Reactome | 2 / 32 | 20.9× | 4.09e-3 | 3.94e-2 ✓ sig. |
| Apoptosis | KEGG | 3 / 137 | 7.3× | 7.88e-3 | 6.10e-2 |
| Biotin metabolism | KEGG | 1 / 3 | 111× | 8.97e-3 | 6.62e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| response to testosterone | GO:0033574 | 4 / 36 | 57.7× | 6.54e-7 | 5.97e-5 ✓ sig. |
| male gonad development | GO:0008584 | 5 / 117 | 22.2× | 2.85e-6 | 1.97e-4 ✓ sig. |
| hypothalamus development | GO:0021854 | 3 / 15 | 104× | 2.94e-6 | 2.02e-4 ✓ sig. |
| regulation of developmental growth | GO:0048638 | 2 / 2 | 519× | 3.61e-6 | 2.38e-4 ✓ sig. |
| male genitalia development | GO:0030539 | 3 / 19 | 82.0× | 6.23e-6 | 3.70e-4 ✓ sig. |
| embryonic brain development | GO:1990403 | 3 / 20 | 77.9× | 7.32e-6 | 4.21e-4 ✓ sig. |
| positive regulation of epithelial cell proliferation involved in prostate gland development | GO:0060769 | 2 / 3 | 346× | 1.08e-5 | 5.74e-4 ✓ sig. |
| hippocampus development | GO:0021766 | 4 / 74 | 28.1× | 1.21e-5 | 6.27e-4 ✓ sig. |
| morphogenesis of an epithelial fold | GO:0060571 | 2 / 4 | 260× | 2.16e-5 | 9.85e-4 ✓ sig. |
| face morphogenesis | GO:0060325 | 3 / 33 | 47.2× | 3.44e-5 | 1.40e-3 ✓ sig. |
| epithelial cell differentiation involved in prostate gland development | GO:0060742 | 2 / 5 | 208× | 3.60e-5 | 1.45e-3 ✓ sig. |
| establishment of blood-retinal barrier | GO:1990963 | 2 / 6 | 173× | 5.39e-5 | 1.97e-3 ✓ sig. |
| neuron differentiation | GO:0030182 | 5 / 222 | 11.7× | 6.32e-5 | 2.21e-3 ✓ sig. |
| androgen biosynthetic process | GO:0006702 | 2 / 9 | 115× | 1.29e-4 | 3.77e-3 ✓ sig. |
| heart development | GO:0007507 | 5 / 273 | 9.5× | 1.67e-4 | 4.57e-3 ✓ sig. |