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 363

5 diseases · 8 shared-gene connections
5 Diseases
13 Unique genes
0.189 Avg. similarity score
46,xy disorder of sex developmen Most-connected disease (4 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 ⇵
46,xy disorder of sex developmen 4 4 7
Disorders of sex development 4 4 6
17 alpha-hydroxyprogesterone aldolase deficiency 3 3 2
Male pseudohypopituitarism 3 3 4
17-beta-hydroxysteroid dehydrogenase deficiency 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AKR1C2 4 / 5 17 alpha-hydroxyprogesterone aldolase deficiency, 46,xy disorder of sex developmen, Disorders of sex development, Male pseudohypopituitarism
AKR1C4 3 / 5 17 alpha-hydroxyprogesterone aldolase deficiency, 46,xy disorder of sex developmen, Male pseudohypopituitarism
HSD17B3 3 / 5 17-beta-hydroxysteroid dehydrogenase deficiency, 46,xy disorder of sex developmen, Disorders of sex development
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 ⇵
Steroid hormone biosynthesis
AKR1C2, AKR1C4, HSD17B3, SRD5A2, CYP17A1, AKR1C1, AKR1C3
 KEGG 7 / 63 103× 1.30e-13 3.22e-11 ✓ sig.
Androgen biosynthesis
HSD17B3, SRD5A2, CYP17A1, LHB
 Reactome 4 / 11 336× 2.71e-10 3.54e-8 ✓ sig.
Synthesis of bile acids and bile salts via 24-hydroxycholesterol
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 Reactome 4 / 14 264× 8.21e-10 9.43e-8 ✓ sig.
Synthesis of bile acids and bile salts via 27-hydroxycholesterol
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 Reactome 4 / 15 246× 1.12e-9 1.24e-7 ✓ sig.
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 Reactome 4 / 24 154× 8.66e-9 7.73e-7 ✓ sig.
Ovarian steroidogenesis
CYP17A1, AKR1C3, LHCGR, LHB
 KEGG 4 / 52 71.1× 2.17e-7 1.28e-5 ✓ sig.
Retinoid metabolism and transport
AKR1C4, AKR1C1, AKR1C3
 Reactome 3 / 41 67.6× 1.03e-5 3.44e-4 ✓ sig.
Prolactin signaling pathway
CYP17A1, LHCGR, LHB
 KEGG 3 / 71 39.0× 5.43e-5 1.37e-3 ✓ sig.
Hormone signaling
AMH, LHCGR, AMHR2, LHB
 KEGG 4 / 219 16.9× 6.76e-5 1.63e-3 ✓ sig.
Hormone ligand-binding receptors
LHCGR, LHB
 Reactome 2 / 12 154× 7.10e-5 1.70e-3 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 KEGG 4 / 227 16.3× 7.77e-5 1.83e-3 ✓ sig.
Signaling by BMP
AMH, AMHR2
 Reactome 2 / 28 66.0× 4.02e-4 6.74e-3 ✓ sig.
Metabolic pathways
AKR1C2, AKR1C4, HSD17B3, SRD5A2, CYP17A1, AKR1C1, AKR1C3
 KEGG 7 / 1,563 4.1× 5.23e-4 8.24e-3 ✓ sig.
Defective CYP17A1 causes Adrenal hyperplasia 5 (AH5)
CYP17A1
 Reactome 1 / 1 924× 1.08e-3 1.44e-2 ✓ sig.
cAMP signaling pathway
AMH, LHCGR, LHB
 KEGG 3 / 226 12.3× 1.64e-3 1.97e-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 ⇵
progesterone metabolic process
AKR1C2, AKR1C4, CYP17A1, AKR1C1, AKR1C3
 GO:0042448 5 / 10 719× 1.71e-14 1.07e-11 ✓ sig.
cellular response to jasmonic acid stimulus
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0071395 4 / 4 1,437× 1.41e-13 7.53e-11 ✓ sig.
hormone metabolic process
AKR1C2, AKR1C4, CYP17A1, AKR1C1, AKR1C3
 GO:0042445 5 / 25 287× 3.58e-12 1.44e-9 ✓ sig.
sex differentiation
DMRT1, SRD5A2, CYP17A1, AMH, AMHR2
 GO:0007548 5 / 26 276× 4.43e-12 1.75e-9 ✓ sig.
daunorubicin metabolic process
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0044597 4 / 9 639× 1.77e-11 6.14e-9 ✓ sig.
doxorubicin metabolic process
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0044598 4 / 10 575× 2.95e-11 9.58e-9 ✓ sig.
male gonad development
DMRT1, SRD5A2, AKR1C3, LHCGR, AMHR2, LHB
 GO:0008584 6 / 117 73.7× 8.76e-11 2.54e-8 ✓ sig.
steroid metabolic process
AKR1C2, AKR1C4, SRD5A2, CYP17A1, AKR1C1, AKR1C3
 GO:0008202 6 / 135 63.9× 2.09e-10 5.55e-8 ✓ sig.
monocarboxylic acid metabolic process
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0032787 4 / 17 338× 3.33e-10 8.41e-8 ✓ sig.
alcohol metabolic process
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0006066 4 / 18 319× 4.28e-10 1.05e-7 ✓ sig.
prostaglandin metabolic process
AKR1C2, AKR1C4, AKR1C1, AKR1C3
 GO:0006693 4 / 30 192× 3.82e-9 7.35e-7 ✓ sig.
testosterone biosynthetic process
HSD17B3, SRD5A2, AKR1C3
 GO:0061370 3 / 6 719× 5.25e-9 9.75e-7 ✓ sig.
androgen biosynthetic process
HSD17B3, SRD5A2, CYP17A1
 GO:0006702 3 / 9 479× 2.20e-8 3.40e-6 ✓ sig.
male genitalia development
HSD17B3, SRD5A2, LHCGR
 GO:0030539 3 / 19 227× 2.53e-7 2.65e-5 ✓ sig.
lipid metabolic process
AKR1C2, AKR1C4, HSD17B3, SRD5A2, CYP17A1, AKR1C1, AKR1C3
 GO:0006629 7 / 840 12.0× 4.89e-7 4.60e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
17 alpha-hydroxyprogesterone aldolase deficiency Male pseudohypopituitarism 0.400 2 5.06e-8 3.92e-7 ✓ sig.
17 alpha-hydroxyprogesterone aldolase deficiency 46,xy disorder of sex developmen 0.250 2 1.77e-7 1.25e-6 ✓ sig.
46,xy disorder of sex developmen Male pseudohypopituitarism 0.200 2 1.06e-6 6.56e-6 ✓ sig.
46,xy disorder of sex developmen Disorders of sex development 0.167 2 2.65e-6 1.53e-5 ✓ sig.
17-beta-hydroxysteroid dehydrogenase deficiency Disorders of sex development 0.143 1 3.90e-4 8.52e-4 ✓ sig.
17-beta-hydroxysteroid dehydrogenase deficiency 46,xy disorder of sex developmen 0.125 1 4.55e-4 9.55e-4 ✓ sig.
17 alpha-hydroxyprogesterone aldolase deficiency Disorders of sex development 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Disorders of sex development Male pseudohypopituitarism 0.100 1 1.56e-3 2.36e-3 ✓ sig.