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 183
8
Diseases
12
Unique genes
0.189
Avg. similarity score
46,xx ovotesticular disorder of sex development
Most-connected disease (5 links)
Disease
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46,xx ovotesticular disorder of sex development
46, xy disorder of sex development
46,xx sex reversal
NR5A1-related sex development disorder
46 XY differences of sex development
MCM9-related gametogenic failure
NR2F2 related multiple congenital anomalies/dysmorphic syndrome
Testotoxicosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 46,xx ovotesticular disorder of sex development | 5 | 5 | 6 |
| 46, xy disorder of sex development | 4 | 4 | 3 |
| 46,xx sex reversal | 4 | 4 | 5 |
| NR5A1-related sex development disorder | 3 | 3 | 1 |
| 46 XY differences of sex development | 1 | 1 | 1 |
| MCM9-related gametogenic failure | 1 | 1 | 1 |
| NR2F2 related multiple congenital anomalies/dysmorphic syndrome | 1 | 1 | 1 |
| Testotoxicosis | 1 | 1 | 4 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NR5A1 | 4 / 8 | 46, xy disorder of sex development, 46,xx ovotesticular disorder of sex development, 46,xx sex reversal, NR5A1-related sex development disorder |
| DMRT1 | 2 / 8 | 46 XY differences of sex development, 46,xx ovotesticular disorder of sex development |
| LHCGR | 2 / 8 | 46, xy disorder of sex development, Testotoxicosis |
| MCM9 | 2 / 8 | 46,xx ovotesticular disorder of sex development, MCM9-related gametogenic failure |
| NR2F2 | 2 / 8 | 46,xx sex reversal, NR2F2 related multiple congenital anomalies/dysmorphic syndrome |
| SOX3 | 2 / 8 | 46,xx ovotesticular disorder of sex development, 46,xx sex reversal |
| SOX9 | 2 / 8 | 46,xx ovotesticular disorder of sex development, 46,xx sex reversal |
| SRY | 2 / 8 | 46,xx ovotesticular disorder of sex development, 46,xx sex reversal |
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 ⇵ |
|---|---|---|---|---|---|
| Deactivation of the beta-catenin transactivating complex | Reactome | 3 / 42 | 71.5× | 8.56e-6 | 2.95e-4 ✓ sig. |
| Glycoprotein hormones | Reactome | 2 / 12 | 167× | 6.01e-5 | 1.48e-3 ✓ sig. |
| Ovarian steroidogenesis | KEGG | 2 / 52 | 38.5× | 1.18e-3 | 1.53e-2 ✓ sig. |
| Cortisol synthesis and secretion | KEGG | 2 / 65 | 30.8× | 1.84e-3 | 2.14e-2 ✓ sig. |
| Antagonism of Activin by Follistatin | Reactome | 1 / 4 | 250× | 3.99e-3 | 3.77e-2 ✓ sig. |
| Defective CYP11A1 causes Adrenal insufficiency, congenital, with 46,XY sex reversal (AICSR) | Reactome | 1 / 4 | 250× | 3.99e-3 | 3.77e-2 ✓ sig. |
| Cushing syndrome | KEGG | 2 / 155 | 12.9× | 1.00e-2 | 6.86e-2 |
| Signaling by Activin | Reactome | 1 / 11 | 91.0× | 1.09e-2 | 7.25e-2 |
| Transcriptional regulation by RUNX2 | Reactome | 1 / 12 | 83.4× | 1.19e-2 | 7.61e-2 |
| Hormone ligand-binding receptors | Reactome | 1 / 12 | 83.4× | 1.19e-2 | 7.61e-2 |
| Pregnenolone biosynthesis | Reactome | 1 / 12 | 83.4× | 1.19e-2 | 7.61e-2 |
| Transcriptional regulation of pluripotent stem cells | Reactome | 1 / 17 | 58.9× | 1.69e-2 | 9.37e-2 |
| cAMP signaling pathway | KEGG | 2 / 226 | 8.9× | 2.05e-2 | 1.04e-1 |
| Endogenous sterols | Reactome | 1 / 25 | 40.0× | 2.47e-2 | 1.16e-1 |
| SUMOylation of intracellular receptors | Reactome | 1 / 27 | 37.1× | 2.67e-2 | 1.21e-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 | 4 / 8 | 779× | 6.81e-12 | 2.60e-9 ✓ sig. |
| male gonad development | GO:0008584 | 6 / 117 | 79.9× | 4.74e-11 | 1.47e-8 ✓ sig. |
| male sex determination | GO:0030238 | 4 / 12 | 519× | 4.81e-11 | 1.49e-8 ✓ sig. |
| female gonad development | GO:0008585 | 4 / 27 | 231× | 1.70e-9 | 3.59e-7 ✓ sig. |
| Sertoli cell differentiation | GO:0060008 | 3 / 9 | 519× | 1.70e-8 | 2.71e-6 ✓ sig. |
| negative regulation of follicle-stimulating hormone secretion | GO:0046882 | 2 / 3 | 1,038× | 1.13e-6 | 9.16e-5 ✓ sig. |
| response to gonadotropin | GO:0034698 | 2 / 4 | 779× | 2.27e-6 | 1.59e-4 ✓ sig. |
| ovarian follicle development | GO:0001541 | 3 / 47 | 99.4× | 3.23e-6 | 2.12e-4 ✓ sig. |
| positive regulation of follicle-stimulating hormone secretion | GO:0046881 | 2 / 6 | 519× | 5.66e-6 | 3.31e-4 ✓ sig. |
| sex determination | GO:0007530 | 2 / 8 | 389× | 1.06e-5 | 5.43e-4 ✓ sig. |
| cell differentiation | GO:0030154 | 6 / 1,051 | 8.9× | 2.15e-5 | 9.53e-4 ✓ sig. |
| Sertoli cell development | GO:0060009 | 2 / 13 | 240× | 2.94e-5 | 1.20e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 6 / 1,208 | 7.7× | 4.75e-5 | 1.73e-3 ✓ sig. |
| oocyte development | GO:0048599 | 2 / 19 | 164× | 6.43e-5 | 2.17e-3 ✓ sig. |
| seminiferous tubule development | GO:0072520 | 2 / 21 | 148× | 7.88e-5 | 2.53e-3 ✓ sig. |