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 35

16 diseases · 39 shared-gene connections
16 Diseases
50 Unique genes
0.197 Avg. similarity score
46,xy gonadal dysgenesis Most-connected disease (10 links)
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Disease Searched: Ovarian dysgenesis 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 gonadal dysgenesis 10 10 15
46,xx ovotesticular disorder of sex development 8 8 6
46,xx sex reversal 8 8 5
46,xy partial gonadal dysgenesis 7 7 8
46,xy sex reversal 7 7 7
Swyer syndrome 7 7 10
NR5A1-related sex development disorder 5 5 1
Ovarian dysgenesis 5 5 12
46, xy disorder of sex development 4 4 3
Gonadal dysgenesis 4 4 28
Testicular regression syndrome 4 4 1
Ovarian teratoma 3 3 1
MCM9-related gametogenic failure 2 2 1
Ovarian hyperstimulation syndrome 2 2 2
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 9 / 16 46, xy disorder of sex development, 46,xx ovotesticular disorder of sex development, 46,xx sex reversal, 46,xy gonadal dysgenesis and 5 more
SRY 7 / 16 46,xx ovotesticular disorder of sex development, 46,xx sex reversal, 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis and 3 more
DHX37 6 / 16 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Gonadal dysgenesis and 2 more
SOX9 5 / 16 46,xx ovotesticular disorder of sex development, 46,xx sex reversal, 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis and 1 more
BMP15 4 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis, Ovarian teratoma
FSHR 4 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis, Ovarian hyperstimulation syndrome
MAP3K1 4 / 16 46,xy gonadal dysgenesis, 46,xy partial gonadal dysgenesis, 46,xy sex reversal, Swyer syndrome
CBX2 3 / 16 46,xy gonadal dysgenesis, 46,xy sex reversal, Swyer syndrome
DHH 3 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Swyer syndrome
MCM9 3 / 16 46,xx ovotesticular disorder of sex development, MCM9-related gametogenic failure, Ovarian dysgenesis
MRPS22 3 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis
NUP107 3 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis
PSMC3IP 3 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis
SPIDR 3 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis, Ovarian dysgenesis
BNC1 2 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis
DMRT1 2 / 16 46,xx ovotesticular disorder of sex development, Swyer syndrome
LHCGR 2 / 16 46, xy disorder of sex development, Testotoxicosis
NR0B1 2 / 16 46,xy sex reversal, Swyer syndrome
NR2F2 2 / 16 46,xx sex reversal, NR2F2 related multiple congenital anomalies/dysmorphic syndrome
POLR3H 2 / 16 46,xy gonadal dysgenesis, Gonadal dysgenesis
SOX3 2 / 16 46,xx ovotesticular disorder of sex development, 46,xx sex reversal
ZFPM2 2 / 16 46,xy partial gonadal dysgenesis, 46,xy sex reversal
ZSWIM7 2 / 16 Gonadal dysgenesis, Ovarian dysgenesis
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
BMP15, FSHR, CYP11A1, LHCGR
 KEGG 4 / 52 18.5× 6.21e-5 1.54e-3 ✓ sig.
Deactivation of the beta-catenin transactivating complex
SOX3, SOX9, SRY
 Reactome 3 / 42 17.2× 6.95e-4 1.05e-2 ✓ sig.
Glycoprotein hormones
INHA, INHBB
 Reactome 2 / 12 40.0× 1.09e-3 1.48e-2 ✓ sig.
Hormone ligand-binding receptors
FSHR, LHCGR
 Reactome 2 / 12 40.0× 1.09e-3 1.48e-2 ✓ sig.
Nuclear Receptor transcription pathway
NR5A1, NR0B1, ESR2
 Reactome 3 / 52 13.9× 1.30e-3 1.70e-2 ✓ sig.
Mitochondrial tRNA aminoacylation
HARS2, LARS2
 Reactome 2 / 14 34.3× 1.50e-3 1.89e-2 ✓ sig.
Cortisol synthesis and secretion
NR5A1, NR0B1, CYP11A1
 KEGG 3 / 65 11.1× 2.47e-3 2.73e-2 ✓ sig.
SUMOylation of RNA binding proteins
NUP107, CBX2
 Reactome 2 / 47 10.2× 1.63e-2 9.45e-2
Antagonism of Activin by Follistatin
INHBB
 Reactome 1 / 4 60.1× 1.66e-2 9.50e-2
Defective CYP11A1 causes Adrenal insufficiency, congenital, with 46,XY sex reversal (AICSR)
CYP11A1
 Reactome 1 / 4 60.1× 1.66e-2 9.50e-2
HHAT G278V abrogates palmitoylation of Hh-Np
DHH
 Reactome 1 / 4 60.1× 1.66e-2 9.50e-2
ChREBP activates metabolic gene expression
MLX
 Reactome 1 / 7 34.3× 2.88e-2 1.30e-1
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
GATA4
 Reactome 1 / 7 34.3× 2.88e-2 1.30e-1
Release of Hh-Np from the secreting cell
DHH
 Reactome 1 / 7 34.3× 2.88e-2 1.30e-1
Ligand-receptor interactions
DHH
 Reactome 1 / 7 34.3× 2.88e-2 1.30e-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
NR5A1, DMRT1, SOX9, SRY, DHX37, ZFPM2, WT1
 GO:2000020 7 / 8 327× 5.06e-18 5.94e-15 ✓ sig.
male sex determination
NR5A1, DMRT1, SOX9, SRY, DHH, NR0B1
 GO:0030238 6 / 12 187× 2.45e-13 1.24e-10 ✓ sig.
male gonad development
FSHR, NR5A1, DMRT1, SOX9, GATA4, NR0B1, LHCGR, INHA, INHBB, WT1
 GO:0008584 10 / 117 31.9× 5.21e-13 2.48e-10 ✓ sig.
female gonad development
FSHR, NR5A1, NUP107, NR2F2, LHCGR, INHBB
 GO:0008585 6 / 27 83.1× 7.63e-11 2.22e-8 ✓ sig.
female gamete generation
BMP15, FSHR, MCM9, MSH4, HROB
 GO:0007292 5 / 21 89.0× 2.20e-9 4.39e-7 ✓ sig.
sex determination
NR5A1, SOX3, NR0B1, WT1
 GO:0007530 4 / 8 187× 3.15e-9 6.02e-7 ✓ sig.
Sertoli cell differentiation
NR5A1, DMRT1, SOX9, NR0B1
 GO:0060008 4 / 9 166× 5.66e-9 1.01e-6 ✓ sig.
negative regulation of female gonad development
NR5A1, ZFPM2, WT1
 GO:2000195 3 / 3 374× 1.80e-8 2.81e-6 ✓ sig.
Sertoli cell development
FSHR, DMRT1, SOX9, HSD17B4
 GO:0060009 4 / 13 115× 3.18e-8 4.60e-6 ✓ sig.
ovarian follicle development
FSHR, LHCGR, INHA, INHBB, MSH4
 GO:0001541 5 / 47 39.8× 1.57e-7 1.80e-5 ✓ sig.
positive regulation of transcription by RNA polymerase II
NR5A1, DMRT1, SOX3, SOX9, SRY, NR2F2, GATA4, WWOX, ZFPM2, WT1, FIGLA, MLX
 GO:0045944 14 / 1,208 4.3× 2.14e-6 1.55e-4 ✓ sig.
Leydig cell differentiation
NR5A1, DHH, NR0B1
 GO:0033327 3 / 11 102× 2.93e-6 2.00e-4 ✓ sig.
gonad development
FSHR, NR0B1, WT1
 GO:0008406 3 / 16 70.1× 9.85e-6 5.24e-4 ✓ sig.
spermatogenesis
BNC1, FSHR, DMRT1, SOX9, NR0B1, LHCGR, INHBB, MSH4, SOHLH1
 GO:0007283 9 / 556 6.0× 1.45e-5 7.07e-4 ✓ sig.
cell differentiation
BNC1, DMRT1, SOX9, SRY, NR2F2, CBX2, GATA4, ZFPM2, INHA, INHBB, FIGLA, SOHLH1
 GO:0030154 12 / 1,051 4.3× 1.56e-5 7.52e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
46,xy gonadal dysgenesis Gonadal dysgenesis 0.375 12 3.74e-32 1.23e-30 ✓ sig.
46,xy gonadal dysgenesis Swyer syndrome 0.368 7 1.90e-20 3.71e-19 ✓ sig.
46,xy sex reversal Swyer syndrome 0.500 6 7.95e-20 1.51e-18 ✓ sig.
Gonadal dysgenesis Ovarian dysgenesis 0.206 7 2.29e-17 3.83e-16 ✓ sig.
46,xy partial gonadal dysgenesis 46,xy sex reversal 0.455 5 1.63e-16 2.59e-15 ✓ sig.
46,xy gonadal dysgenesis Ovarian dysgenesis 0.273 6 2.49e-16 3.90e-15 ✓ sig.
46,xy partial gonadal dysgenesis Swyer syndrome 0.357 5 1.96e-15 2.89e-14 ✓ sig.
46,xy gonadal dysgenesis 46,xy sex reversal 0.278 5 8.74e-15 1.24e-13 ✓ sig.
46,xy gonadal dysgenesis 46,xy partial gonadal dysgenesis 0.263 5 2.33e-14 3.19e-13 ✓ sig.
46,xx ovotesticular disorder of sex development 46,xx sex reversal 0.500 4 3.20e-14 4.32e-13 ✓ sig.
46,xx ovotesticular disorder of sex development Swyer syndrome 0.308 4 1.34e-12 1.62e-11 ✓ sig.
46,xx sex reversal 46,xy partial gonadal dysgenesis 0.273 3 9.20e-10 8.38e-9 ✓ sig.
Gonadal dysgenesis Swyer syndrome 0.114 4 1.82e-9 1.62e-8 ✓ sig.
46,xx ovotesticular disorder of sex development 46,xy partial gonadal dysgenesis 0.250 3 1.84e-9 1.63e-8 ✓ sig.
46,xx sex reversal Swyer syndrome 0.231 3 1.97e-9 1.74e-8 ✓ sig.
46,xx sex reversal 46,xy gonadal dysgenesis 0.167 3 7.47e-9 6.23e-8 ✓ sig.
46,xx ovotesticular disorder of sex development 46,xy gonadal dysgenesis 0.158 3 1.49e-8 1.18e-7 ✓ sig.
46,xx sex reversal 46,xy sex reversal 0.182 2 1.77e-6 9.99e-6 ✓ sig.
46,xx ovotesticular disorder of sex development 46,xy sex reversal 0.167 2 2.65e-6 1.45e-5 ✓ sig.
46, xy disorder of sex development NR5A1-related sex development disorder 0.250 1 1.95e-4 5.32e-4 ✓ sig.
46,xx sex reversal NR2F2 related multiple congenital anomalies/dysmorphic syndrome 0.167 1 3.25e-4 7.68e-4 ✓ sig.
46,xx sex reversal NR5A1-related sex development disorder 0.167 1 3.25e-4 7.68e-4 ✓ sig.
46,xx ovotesticular disorder of sex development MCM9-related gametogenic failure 0.143 1 3.90e-4 8.64e-4 ✓ sig.
46,xx ovotesticular disorder of sex development NR5A1-related sex development disorder 0.143 1 3.90e-4 8.64e-4 ✓ sig.
46,xy sex reversal Testicular regression syndrome 0.125 1 4.55e-4 9.70e-4 ✓ sig.
46,xy sex reversal NR5A1-related sex development disorder 0.125 1 4.55e-4 9.70e-4 ✓ sig.
46,xy partial gonadal dysgenesis Testicular regression syndrome 0.111 1 5.20e-4 1.06e-3 ✓ sig.
46,xy partial gonadal dysgenesis NR5A1-related sex development disorder 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Swyer syndrome Testicular regression syndrome 0.091 1 6.49e-4 1.24e-3 ✓ sig.
46, xy disorder of sex development Testotoxicosis 0.143 1 7.79e-4 1.40e-3 ✓ sig.
Ovarian dysgenesis Ovarian teratoma 0.077 1 7.79e-4 1.40e-3 ✓ sig.
MCM9-related gametogenic failure Ovarian dysgenesis 0.077 1 7.79e-4 1.40e-3 ✓ sig.
46, xy disorder of sex development 46,xx sex reversal 0.125 1 9.74e-4 1.66e-3 ✓ sig.
46,xy gonadal dysgenesis Ovarian teratoma 0.063 1 9.74e-4 1.66e-3 ✓ sig.
46,xy gonadal dysgenesis Testicular regression syndrome 0.063 1 9.74e-4 1.66e-3 ✓ sig.
46, xy disorder of sex development 46,xx ovotesticular disorder of sex development 0.111 1 1.17e-3 1.89e-3 ✓ sig.
Ovarian dysgenesis Ovarian hyperstimulation syndrome 0.071 1 1.56e-3 2.37e-3 ✓ sig.
Gonadal dysgenesis Ovarian teratoma 0.034 1 1.82e-3 2.68e-3 ✓ sig.
46,xy gonadal dysgenesis Ovarian hyperstimulation syndrome 0.059 1 1.95e-3 2.83e-3 ✓ sig.