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 538
5
Diseases
15
Unique genes
0.250
Avg. similarity score
Amenorrhea
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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Amenorrhea
Hypogonadotropic hypogonadism 24 with or without anosmia
Hypogonadotropic hypogonadism 24 without anosmia
Isolated follicle-stimulating hormone deficiency
Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Amenorrhea | 4 | 4 | 15 |
| Hypogonadotropic hypogonadism 24 with or without anosmia | 3 | 3 | 1 |
| Hypogonadotropic hypogonadism 24 without anosmia | 3 | 3 | 1 |
| Isolated follicle-stimulating hormone deficiency | 3 | 3 | 1 |
| Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| FSHB | 4 / 5 | Amenorrhea, Hypogonadotropic hypogonadism 24 with or without anosmia, Hypogonadotropic hypogonadism 24 without anosmia, Isolated follicle-stimulating hormone deficiency |
| VPS50 | 2 / 5 | Amenorrhea, Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis |
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 ⇵ |
|---|---|---|---|---|---|
| Ovarian steroidogenesis | KEGG | 4 / 52 | 61.6× | 4.12e-7 | 1.93e-5 ✓ sig. |
| Hormone signaling | KEGG | 4 / 219 | 14.6× | 1.25e-4 | 2.27e-3 ✓ sig. |
| ADORA2B mediated anti-inflammatory cytokines production | Reactome | 3 / 128 | 18.8× | 4.90e-4 | 6.58e-3 ✓ sig. |
| G alpha (s) signalling events | Reactome | 3 / 140 | 17.2× | 6.37e-4 | 8.05e-3 ✓ sig. |
| Defective CYP17A1 causes Adrenal hyperplasia 5 (AH5) | Reactome | 1 / 1 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Defective CYP19A1 causes Aromatase excess syndrome (AEXS) | Reactome | 1 / 1 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Cytochrome P450 - arranged by substrate type | Reactome | 1 / 1 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Steroid hormone biosynthesis | KEGG | 2 / 63 | 25.4× | 2.72e-3 | 2.38e-2 ✓ sig. |
| Cortisol synthesis and secretion | KEGG | 2 / 65 | 24.6× | 2.89e-3 | 2.49e-2 ✓ sig. |
| Prolactin signaling pathway | KEGG | 2 / 71 | 22.6× | 3.44e-3 | 2.81e-2 ✓ sig. |
| LDL remodeling | Reactome | 1 / 3 | 267× | 3.74e-3 | 2.98e-2 ✓ sig. |
| Scavenging by Class H Receptors | Reactome | 1 / 4 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| GnRH signaling pathway | KEGG | 2 / 93 | 17.2× | 5.83e-3 | 4.04e-2 ✓ sig. |
| Chylomicron clearance | Reactome | 1 / 5 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| Scavenging by Class B Receptors | Reactome | 1 / 5 | 160× | 6.23e-3 | 4.21e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| mammary gland development | GO:0030879 | 2 / 37 | 67.3× | 3.94e-4 | 8.09e-3 ✓ sig. |
| positive regulation of gene expression | GO:0010628 | 4 / 504 | 9.9× | 5.63e-4 | 1.03e-2 ✓ sig. |
| deoxyribonucleoside catabolic process | GO:0046121 | 1 / 1 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| deoxyribose phosphate catabolic process | GO:0046386 | 1 / 1 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| nitrate catabolic process | GO:0043602 | 1 / 1 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| positive regulation of growth plate cartilage chondrocyte proliferation | GO:0061913 | 1 / 1 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| positive regulation of steroid hormone biosynthetic process | GO:0090031 | 1 / 1 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| steroid biosynthetic process | GO:0006694 | 2 / 65 | 38.3× | 1.21e-3 | 1.63e-2 ✓ sig. |
| activation of protein kinase A activity | GO:0034199 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of estradiol secretion | GO:2000866 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of steroid biosynthetic process | GO:0010893 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| nitric oxide catabolic process | GO:0046210 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| organofluorine metabolic process | GO:0090346 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of lactation | GO:1903489 | 1 / 2 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| female pregnancy | GO:0007565 | 2 / 80 | 31.1× | 1.83e-3 | 2.04e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Hypogonadotropic hypogonadism 24 with or without anosmia | Isolated follicle-stimulating hormone deficiency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Hypogonadotropic hypogonadism 24 with or without anosmia | Hypogonadotropic hypogonadism 24 without anosmia | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Hypogonadotropic hypogonadism 24 without anosmia | Isolated follicle-stimulating hormone deficiency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Amenorrhea | Hypogonadotropic hypogonadism 24 with or without anosmia | 0.063 | 1 | 9.68e-4 | 1.50e-3 ✓ sig. |
| Amenorrhea | Hypogonadotropic hypogonadism 24 without anosmia | 0.063 | 1 | 9.68e-4 | 1.50e-3 ✓ sig. |
| Amenorrhea | Isolated follicle-stimulating hormone deficiency | 0.063 | 1 | 9.68e-4 | 1.50e-3 ✓ sig. |
| Amenorrhea | Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis | 0.063 | 1 | 9.68e-4 | 1.50e-3 ✓ sig. |