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 149
9
Diseases
43
Unique genes
0.204
Avg. similarity score
46,xy gonadal dysgenesis
Most-connected disease (8 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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46,xy gonadal dysgenesis
Swyer syndrome
46,xy partial gonadal dysgenesis
46,xy sex reversal
Gonadal dysgenesis
Ovarian dysgenesis
Testicular regression syndrome
Ovarian teratoma
Ovarian hyperstimulation syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 46,xy gonadal dysgenesis | 8 | 8 | 15 |
| Swyer syndrome | 5 | 5 | 10 |
| 46,xy partial gonadal dysgenesis | 4 | 4 | 8 |
| 46,xy sex reversal | 4 | 4 | 7 |
| Gonadal dysgenesis | 4 | 4 | 28 |
| Ovarian dysgenesis | 4 | 4 | 12 |
| Testicular regression syndrome | 4 | 4 | 1 |
| Ovarian teratoma | 3 | 3 | 1 |
| Ovarian hyperstimulation syndrome | 2 | 2 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DHX37 | 6 / 9 | 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Gonadal dysgenesis and 2 more |
| NR5A1 | 5 / 9 | 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Gonadal dysgenesis and 1 more |
| SRY | 5 / 9 | 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Gonadal dysgenesis and 1 more |
| BMP15 | 4 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis, Ovarian teratoma |
| FSHR | 4 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis, Ovarian hyperstimulation syndrome |
| MAP3K1 | 4 / 9 | 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Swyer syndrome |
| CBX2 | 3 / 9 | 46,xy gonadal dysgenesis, 46,xy sex reversal, Swyer syndrome |
| DHH | 3 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Swyer syndrome |
| MRPS22 | 3 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis |
| NUP107 | 3 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis |
| PSMC3IP | 3 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis |
| SOX9 | 3 / 9 | 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, Swyer syndrome |
| SPIDR | 3 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis |
| BNC1 | 2 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis |
| NR0B1 | 2 / 9 | 46,xy sex reversal, Swyer syndrome |
| POLR3H | 2 / 9 | 46,xy gonadal dysgenesis, Gonadal dysgenesis |
| ZFPM2 | 2 / 9 | 46,xy partial gonadal dysgenesis, 46,xy sex reversal |
| ZSWIM7 | 2 / 9 | Gonadal dysgenesis, Ovarian dysgenesis |
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 ⇵ |
|---|---|---|---|---|---|
| Nuclear Receptor transcription pathway | Reactome | 3 / 52 | 16.1× | 8.36e-4 | 1.18e-2 ✓ sig. |
| Mitochondrial tRNA aminoacylation | Reactome | 2 / 14 | 39.9× | 1.11e-3 | 1.46e-2 ✓ sig. |
| Deactivation of the beta-catenin transactivating complex | Reactome | 2 / 42 | 13.3× | 9.85e-3 | 6.80e-2 |
| SUMOylation of RNA binding proteins | Reactome | 2 / 47 | 11.9× | 1.22e-2 | 7.73e-2 |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 69.8× | 1.42e-2 | 8.45e-2 |
| Ovarian steroidogenesis | KEGG | 2 / 52 | 10.7× | 1.48e-2 | 8.66e-2 |
| Cortisol synthesis and secretion | KEGG | 2 / 65 | 8.6× | 2.26e-2 | 1.10e-1 |
| Tight junction | KEGG | 3 / 170 | 4.9× | 2.27e-2 | 1.11e-1 |
| Aminoacyl-tRNA biosynthesis | KEGG | 2 / 66 | 8.5× | 2.32e-2 | 1.12e-1 |
| ChREBP activates metabolic gene expression | Reactome | 1 / 7 | 39.9× | 2.48e-2 | 1.16e-1 |
| Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) | Reactome | 1 / 7 | 39.9× | 2.48e-2 | 1.16e-1 |
| Release of Hh-Np from the secreting cell | Reactome | 1 / 7 | 39.9× | 2.48e-2 | 1.16e-1 |
| Ligand-receptor interactions | Reactome | 1 / 7 | 39.9× | 2.48e-2 | 1.16e-1 |
| SUMOylation of chromatin organization proteins | Reactome | 2 / 70 | 8.0× | 2.59e-2 | 1.19e-1 |
| SUMOylation of DNA damage response and repair proteins | Reactome | 2 / 77 | 7.3× | 3.09e-2 | 1.31e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of male gonad development | GO:2000020 | 7 / 8 | 380× | 1.63e-18 | 2.13e-15 ✓ sig. |
| male sex determination | GO:0030238 | 6 / 12 | 217× | 9.44e-14 | 5.20e-11 ✓ sig. |
| female gamete generation | GO:0007292 | 5 / 21 | 103× | 1.00e-9 | 2.25e-7 ✓ sig. |
| Sertoli cell differentiation | GO:0060008 | 4 / 9 | 193× | 3.04e-9 | 5.96e-7 ✓ sig. |
| male gonad development | GO:0008584 | 7 / 117 | 26.0× | 8.41e-9 | 1.48e-6 ✓ sig. |
| negative regulation of female gonad development | GO:2000195 | 3 / 3 | 435× | 1.13e-8 | 1.90e-6 ✓ sig. |
| Sertoli cell development | GO:0060009 | 4 / 13 | 134× | 1.71e-8 | 2.73e-6 ✓ sig. |
| sex determination | GO:0007530 | 3 / 8 | 163× | 6.30e-7 | 5.69e-5 ✓ sig. |
| Leydig cell differentiation | GO:0033327 | 3 / 11 | 119× | 1.85e-6 | 1.35e-4 ✓ sig. |
| gonad development | GO:0008406 | 3 / 16 | 81.5× | 6.22e-6 | 3.57e-4 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 12 / 1,208 | 4.3× | 1.19e-5 | 5.95e-4 ✓ sig. |
| adrenal gland development | GO:0030325 | 3 / 24 | 54.3× | 2.22e-5 | 9.75e-4 ✓ sig. |
| sex differentiation | GO:0007548 | 3 / 26 | 50.1× | 2.84e-5 | 1.17e-3 ✓ sig. |
| female gonad development | GO:0008585 | 3 / 27 | 48.3× | 3.19e-5 | 1.28e-3 ✓ sig. |
| DNA recombination | GO:0006310 | 4 / 110 | 15.8× | 1.18e-4 | 3.42e-3 ✓ sig. |