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 193

8 diseases · 7 shared-gene connections
8 Diseases
56 Unique genes
0.049 Avg. similarity score
Ovarian cysts Most-connected disease (5 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Ovarian cysts 5 5 35
Amenorrhea 2 2 15
Congenital adrenal hyperplasia 2 2 11
Bosch-boonstra-schaaf optic atrophy syndrome 1 1 1
Cataract-growth hormone deficiency-skeletal dysplasia syndrome 1 1 1
Isolated follicle-stimulating hormone deficiency 1 1 1
amyotrophic lateral sclerosis type 9 1 1 1
immunodeficiency, common variable, 5 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
CYP17A1 3 / 8 Amenorrhea, Congenital adrenal hyperplasia, Ovarian cysts
ANG 2 / 8 amyotrophic lateral sclerosis type 9, Ovarian cysts
CYP19A1 2 / 8 Amenorrhea, Congenital adrenal hyperplasia
FSHB 2 / 8 Amenorrhea, Isolated follicle-stimulating hormone deficiency
IARS2 2 / 8 Cataract-growth hormone deficiency-skeletal dysplasia syndrome, Ovarian cysts
MS4A1 2 / 8 immunodeficiency, common variable, 5, Ovarian cysts
MSH2 2 / 8 Congenital adrenal hyperplasia, Ovarian cysts
NR2F1 2 / 8 Bosch-boonstra-schaaf optic atrophy syndrome, Ovarian cysts
POR 2 / 8 Amenorrhea, Congenital adrenal hyperplasia
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 ⇵
Cortisol synthesis and secretion
ADCY8, CYP17A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR, NR0B1
 KEGG 8 / 65 26.4× 5.46e-10 6.57e-8 ✓ sig.
Ovarian steroidogenesis
ADCY8, CYP17A1, CYP19A1, FSHB, CYP11A1, HSD3B2, STAR
 KEGG 7 / 52 28.9× 3.70e-9 3.61e-7 ✓ sig.
Glucocorticoid biosynthesis
CYP17A1, CYP11B1, CYP21A2, HSD3B2
 Reactome 4 / 10 85.8× 8.72e-8 5.82e-6 ✓ sig.
Steroid hormone biosynthesis
CYP17A1, CYP19A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2
 KEGG 6 / 63 20.4× 4.32e-7 2.36e-5 ✓ sig.
Endogenous sterols
CYP19A1, CYP11A1, CYP11B1, CYP21A2
 Reactome 4 / 25 34.3× 4.99e-6 1.90e-4 ✓ sig.
Cushing syndrome
ADCY8, CYP17A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR
 KEGG 7 / 155 9.7× 7.11e-6 2.52e-4 ✓ sig.
Aldosterone synthesis and secretion
ADCY8, CYP11A1, CYP21A2, HSD3B2, STAR
 KEGG 5 / 98 10.9× 8.97e-5 2.05e-3 ✓ sig.
Mineralocorticoid biosynthesis
CYP21A2, HSD3B2
 Reactome 2 / 6 71.5× 3.17e-4 5.59e-3 ✓ sig.
Androgen biosynthesis
CYP17A1, HSD3B2
 Reactome 2 / 11 39.0× 1.14e-3 1.50e-2 ✓ sig.
Pregnenolone biosynthesis
CYP11A1, STAR
 Reactome 2 / 12 35.7× 1.37e-3 1.72e-2 ✓ sig.
ADORA2B mediated anti-inflammatory cytokines production
ADCY8, CALCR, FSHB, PTGER4
 Reactome 4 / 128 6.7× 2.95e-3 3.04e-2 ✓ sig.
Hormone signaling
ADCY8, CALCR, FSHB, PRL, AGTR2
 KEGG 5 / 219 4.9× 3.46e-3 3.40e-2 ✓ sig.
G alpha (s) signalling events
ADCY8, CALCR, FSHB, PTGER4
 Reactome 4 / 140 6.1× 4.06e-3 3.81e-2 ✓ sig.
Prolactin signaling pathway
CYP17A1, PRL, NFKB1
 KEGG 3 / 71 9.1× 4.39e-3 4.02e-2 ✓ sig.
Defective CYP11B1 causes Adrenal hyperplasia 4 (AH4)
CYP11B1
 Reactome 1 / 1 214× 4.66e-3 4.18e-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 ⇵
steroid biosynthetic process
CYP17A1, CYP19A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR
 GO:0006694 7 / 65 35.9× 8.96e-10 2.03e-7 ✓ sig.
glucocorticoid biosynthetic process
CYP17A1, CYP11A1, CYP11B1, CYP21A2
 GO:0006704 4 / 7 191× 2.51e-9 5.05e-7 ✓ sig.
cortisol biosynthetic process
CYP17A1, CYP11B1, CYP21A2
 GO:0034651 3 / 5 200× 2.54e-7 2.65e-5 ✓ sig.
sterol metabolic process
CYP19A1, CYP11A1, CYP11B1, CYP21A2
 GO:0016125 4 / 22 60.7× 5.08e-7 4.74e-5 ✓ sig.
cellular response to peptide hormone stimulus
POR, CYP11A1, CYP11B1
 GO:0071375 3 / 18 55.6× 2.01e-5 9.03e-4 ✓ sig.
cortisol metabolic process
CYP11A1, CYP11B1
 GO:0034650 2 / 4 167× 5.27e-5 1.88e-3 ✓ sig.
C21-steroid hormone biosynthetic process
CYP11A1, CYP11B1
 GO:0006700 2 / 5 133× 8.77e-5 2.74e-3 ✓ sig.
positive regulation of gene expression
APOB, CALCR, FSHB, RIMS1, CDH3, PRKN, RPL5, SFRP4
 GO:0010628 8 / 504 5.3× 1.21e-4 3.48e-3 ✓ sig.
lipid metabolic process
APOB, CYP17A1, CYP19A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR, TNXB, PTGS1
 GO:0006629 10 / 840 4.0× 1.73e-4 4.56e-3 ✓ sig.
C21-steroid hormone metabolic process
CYP11A1, HSD3B2
 GO:0008207 2 / 7 95.3× 1.83e-4 4.76e-3 ✓ sig.
cholesterol metabolic process
APOB, CYP11A1, CYP11B1, STAR
 GO:0008203 4 / 107 12.5× 2.97e-4 6.66e-3 ✓ sig.
androgen biosynthetic process
CYP17A1, HSD3B2
 GO:0006702 2 / 9 74.2× 3.13e-4 6.93e-3 ✓ sig.
proteoglycan metabolic process
COL11A1, IHH
 GO:0006029 2 / 11 60.7× 4.77e-4 9.29e-3 ✓ sig.
response to hormone
POR, ANG, SFRP4
 GO:0009725 3 / 55 18.2× 5.99e-4 1.08e-2 ✓ sig.
steroid metabolic process
APOB, CYP17A1, CYP11A1, CYP21A2
 GO:0008202 4 / 135 9.9× 7.15e-4 1.22e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Amenorrhea Congenital adrenal hyperplasia 0.125 3 1.23e-7 9.01e-7 ✓ sig.
Congenital adrenal hyperplasia Ovarian cysts 0.044 2 2.73e-4 6.71e-4 ✓ sig.
Amenorrhea Isolated follicle-stimulating hormone deficiency 0.063 1 9.74e-4 1.64e-3 ✓ sig.
amyotrophic lateral sclerosis type 9 Ovarian cysts 0.028 1 2.27e-3 3.18e-3 ✓ sig.
Bosch-boonstra-schaaf optic atrophy syndrome Ovarian cysts 0.028 1 2.27e-3 3.18e-3 ✓ sig.
Cataract-growth hormone deficiency-skeletal dysplasia syndrome Ovarian cysts 0.028 1 2.27e-3 3.18e-3 ✓ sig.
immunodeficiency, common variable, 5 Ovarian cysts 0.028 1 2.27e-3 3.18e-3 ✓ sig.