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 350

5 diseases · 7 shared-gene connections
5 Diseases
23 Unique genes
0.140 Avg. similarity score
Amenorrhea Most-connected disease (4 links)
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Disease Searched: 17,20-lyase deficiency 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 ⇵
Amenorrhea 4 4 15
17,20-lyase deficiency 3 3 1
Congenital adrenal hyperplasia 3 3 11
Steroid 17-alpha-monooxygenase deficiency 3 3 1
Isolated follicle-stimulating hormone deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CYP17A1 4 / 5 17,20-lyase deficiency, Amenorrhea, Congenital adrenal hyperplasia, Steroid 17-alpha-monooxygenase deficiency
CYP19A1 2 / 5 Amenorrhea, Congenital adrenal hyperplasia
FSHB 2 / 5 Amenorrhea, Isolated follicle-stimulating hormone deficiency
POR 2 / 5 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
CYP17A1, ADCY8, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR, NR0B1
 KEGG 8 / 65 64.3× 2.17e-13 4.98e-11 ✓ sig.
Ovarian steroidogenesis
CYP17A1, ADCY8, CYP19A1, FSHB, CYP11A1, HSD3B2, STAR
 KEGG 7 / 52 70.3× 4.36e-12 7.94e-10 ✓ sig.
Steroid hormone biosynthesis
CYP17A1, CYP19A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2
 KEGG 6 / 63 49.7× 1.54e-9 1.57e-7 ✓ sig.
Glucocorticoid biosynthesis
CYP17A1, CYP11B1, CYP21A2, HSD3B2
 Reactome 4 / 10 209× 2.13e-9 2.12e-7 ✓ sig.
Cushing syndrome
CYP17A1, ADCY8, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR
 KEGG 7 / 155 23.6× 1.07e-8 9.02e-7 ✓ sig.
Endogenous sterols
CYP19A1, CYP11A1, CYP11B1, CYP21A2
 Reactome 4 / 25 83.5× 1.26e-7 8.02e-6 ✓ sig.
Aldosterone synthesis and secretion
ADCY8, CYP11A1, CYP21A2, HSD3B2, STAR
 KEGG 5 / 98 26.6× 9.78e-7 4.78e-5 ✓ sig.
Mineralocorticoid biosynthesis
CYP21A2, HSD3B2
 Reactome 2 / 6 174× 5.24e-5 1.35e-3 ✓ sig.
Androgen biosynthesis
CYP17A1, HSD3B2
 Reactome 2 / 11 94.9× 1.91e-4 3.81e-3 ✓ sig.
Pregnenolone biosynthesis
CYP11A1, STAR
 Reactome 2 / 12 87.0× 2.29e-4 4.39e-3 ✓ sig.
Hormone signaling
ADCY8, CALCR, FSHB, PRL
 KEGG 4 / 219 9.5× 7.25e-4 1.09e-2 ✓ sig.
Metabolic pathways
CYP17A1, ADCY8, CYP19A1, DERA, PPCDC, CYP11A1, CYP11B1, CYP21A2, HSD3B2
 KEGG 9 / 1,563 3.0× 1.54e-3 1.93e-2 ✓ sig.
ADORA2B mediated anti-inflammatory cytokines production
ADCY8, CALCR, FSHB
 Reactome 3 / 128 12.2× 1.79e-3 2.15e-2 ✓ sig.
Defective CYP11B1 causes Adrenal hyperplasia 4 (AH4)
CYP11B1
 Reactome 1 / 1 522× 1.92e-3 2.25e-2 ✓ sig.
Defective CYP17A1 causes Adrenal hyperplasia 5 (AH5)
CYP17A1
 Reactome 1 / 1 522× 1.92e-3 2.25e-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 87.5× 1.04e-12 4.67e-10 ✓ sig.
glucocorticoid biosynthetic process
CYP17A1, CYP11A1, CYP11B1, CYP21A2
 GO:0006704 4 / 7 464× 6.09e-11 1.82e-8 ✓ sig.
sterol metabolic process
CYP19A1, CYP11A1, CYP11B1, CYP21A2
 GO:0016125 4 / 22 148× 1.26e-8 2.05e-6 ✓ sig.
cortisol biosynthetic process
CYP17A1, CYP11B1, CYP21A2
 GO:0034651 3 / 5 487× 1.63e-8 2.58e-6 ✓ sig.
lipid metabolic process
CYP17A1, APOB, CYP19A1, CYP11A1, CYP11B1, CYP21A2, HSD3B2, STAR, TNXB
 GO:0006629 9 / 840 8.7× 3.32e-7 3.35e-5 ✓ sig.
cellular response to peptide hormone stimulus
POR, CYP11A1, CYP11B1
 GO:0071375 3 / 18 135× 1.31e-6 1.04e-4 ✓ sig.
cholesterol metabolic process
APOB, CYP11A1, CYP11B1, STAR
 GO:0008203 4 / 107 30.4× 8.27e-6 4.60e-4 ✓ sig.
cortisol metabolic process
CYP11A1, CYP11B1
 GO:0034650 2 / 4 406× 8.68e-6 4.77e-4 ✓ sig.
C21-steroid hormone biosynthetic process
CYP11A1, CYP11B1
 GO:0006700 2 / 5 325× 1.45e-5 7.07e-4 ✓ sig.
steroid metabolic process
CYP17A1, APOB, CYP11A1, CYP21A2
 GO:0008202 4 / 135 24.1× 2.07e-5 9.39e-4 ✓ sig.
C21-steroid hormone metabolic process
CYP11A1, HSD3B2
 GO:0008207 2 / 7 232× 3.03e-5 1.24e-3 ✓ sig.
androgen biosynthetic process
CYP17A1, HSD3B2
 GO:0006702 2 / 9 181× 5.19e-5 1.88e-3 ✓ sig.
alcohol metabolic process
CYP11A1, CYP11B1
 GO:0006066 2 / 18 90.3× 2.19e-4 5.48e-3 ✓ sig.
mammary gland development
CYP19A1, PRL
 GO:0030879 2 / 37 43.9× 9.40e-4 1.49e-2 ✓ sig.
positive regulation of cell fate determination
TNXB
 GO:1905935 1 / 1 812× 1.23e-3 1.75e-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 8.55e-7 ✓ sig.
17,20-lyase deficiency Steroid 17-alpha-monooxygenase deficiency 0.500 1 6.49e-5 2.32e-4 ✓ sig.
17,20-lyase deficiency Congenital adrenal hyperplasia 0.083 1 7.14e-4 1.33e-3 ✓ sig.
Congenital adrenal hyperplasia Steroid 17-alpha-monooxygenase deficiency 0.083 1 7.14e-4 1.33e-3 ✓ sig.
17,20-lyase deficiency Amenorrhea 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Amenorrhea Steroid 17-alpha-monooxygenase deficiency 0.063 1 9.74e-4 1.66e-3 ✓ sig.
Amenorrhea Isolated follicle-stimulating hormone deficiency 0.063 1 9.74e-4 1.66e-3 ✓ sig.