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 316

7 diseases · 16 shared-gene connections
7 Diseases
9 Unique genes
0.270 Avg. similarity score
46,xx ovotesticular disorder of sex development Most-connected disease (6 links)
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Disease Searched: X-linked pituitary hormone deficiency with or without intellectual developmental disorder 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,xx ovotesticular disorder of sex development 6 6 6
46,xx sex reversal 5 5 5
Genetic panhypopituitarism 5 5 2
Panhypopituitarism, x-linked 5 5 1
X-linked congenital generalized hypertrichosis 5 5 1
X-linked pituitary hormone deficiency with or without intellectual developmental disorder 5 5 1
Gametogenic failure 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
SOX3 6 / 7 46,xx ovotesticular disorder of sex development, 46,xx sex reversal, Genetic panhypopituitarism, Panhypopituitarism, x-linked and 2 more
MCM9 2 / 7 46,xx ovotesticular disorder of sex development, Gametogenic failure
NR5A1 2 / 7 46,xx ovotesticular disorder of sex development, 46,xx sex reversal
SOX9 2 / 7 46,xx ovotesticular disorder of sex development, 46,xx sex reversal
SRY 2 / 7 46,xx ovotesticular disorder of sex development, 46,xx sex reversal
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 ⇵
Deactivation of the beta-catenin transactivating complex
SOX3, SOX9, SRY
 Reactome 3 / 42 95.3× 3.29e-6 1.08e-4 ✓ sig.
Transcriptional regulation by RUNX2
SOX9
 Reactome 1 / 12 111× 8.96e-3 5.11e-2
Transcriptional regulation of pluripotent stem cells
NR5A1
 Reactome 1 / 17 78.5× 1.27e-2 6.36e-2
SUMOylation of intracellular receptors
NR5A1
 Reactome 1 / 27 49.4× 2.01e-2 8.35e-2
Nuclear Receptor transcription pathway
NR5A1
 Reactome 1 / 52 25.7× 3.83e-2 1.22e-1
Cortisol synthesis and secretion
NR5A1
 KEGG 1 / 65 20.5× 4.77e-2 1.39e-1
Cushing syndrome
NR5A1
 KEGG 1 / 155 8.6× 1.10e-1 2.27e-1
cAMP signaling pathway
SOX9
 KEGG 1 / 226 5.9× 1.57e-1 2.81e-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
DMRT1, NR5A1, SOX9, SRY
 GO:2000020 4 / 8 1,038× 1.73e-12 7.98e-10 ✓ sig.
male sex determination
DMRT1, NR5A1, SOX9, SRY
 GO:0030238 4 / 12 692× 1.23e-11 4.71e-9 ✓ sig.
Sertoli cell differentiation
DMRT1, NR5A1, SOX9
 GO:0060008 3 / 9 692× 6.48e-9 1.21e-6 ✓ sig.
positive regulation of transcription by RNA polymerase II
DMRT1, NR5A1, SOX3, SOX9, SRY, NR2F2, PROP1
 GO:0045944 7 / 1,208 12.0× 1.49e-7 1.75e-5 ✓ sig.
sex determination
NR5A1, SOX3
 GO:0007530 2 / 8 519× 5.76e-6 3.45e-4 ✓ sig.
Sertoli cell development
DMRT1, SOX9
 GO:0060009 2 / 13 319× 1.60e-5 7.65e-4 ✓ sig.
male gonad development
DMRT1, NR5A1, SOX9
 GO:0008584 3 / 117 53.2× 1.95e-5 8.87e-4 ✓ sig.
regulation of transcription by RNA polymerase II
DMRT1, NR5A1, SOX9, SRY, NR2F2, PROP1
 GO:0006357 6 / 1,602 7.8× 2.63e-5 1.11e-3 ✓ sig.
negative regulation of transcription by RNA polymerase II
DMRT1, SOX3, SOX9, NR2F2, PROP1
 GO:0000122 5 / 1,002 10.4× 4.61e-5 1.70e-3 ✓ sig.
central nervous system development
SOX3, SOX9, PROP1
 GO:0007417 3 / 158 39.4× 4.80e-5 1.75e-3 ✓ sig.
sex differentiation
DMRT1, SRY
 GO:0007548 2 / 26 160× 6.66e-5 2.24e-3 ✓ sig.
female gonad development
NR5A1, NR2F2
 GO:0008585 2 / 27 154× 7.19e-5 2.37e-3 ✓ sig.
pituitary gland development
SOX3, PROP1
 GO:0021983 2 / 30 138× 8.91e-5 2.78e-3 ✓ sig.
intracellular receptor signaling pathway
NR5A1, NR2F2
 GO:0030522 2 / 39 106× 1.51e-4 4.10e-3 ✓ sig.
regulation of DNA-templated transcription
DMRT1, NR5A1, SOX3, NR2F2, PROP1
 GO:0006355 5 / 1,454 7.1× 2.74e-4 6.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
46,xx ovotesticular disorder of sex development 46,xx sex reversal 0.500 4 3.13e-14 3.65e-13 ✓ sig.
Panhypopituitarism, x-linked X-linked congenital generalized hypertrichosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Panhypopituitarism, x-linked X-linked pituitary hormone deficiency with or without intellectual developmental disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
X-linked congenital generalized hypertrichosis X-linked pituitary hormone deficiency with or without intellectual developmental disorder 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Genetic panhypopituitarism X-linked congenital generalized hypertrichosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Genetic panhypopituitarism X-linked pituitary hormone deficiency with or without intellectual developmental disorder 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Genetic panhypopituitarism Panhypopituitarism, x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
46,xx sex reversal X-linked congenital generalized hypertrichosis 0.167 1 3.23e-4 6.41e-4 ✓ sig.
46,xx sex reversal Panhypopituitarism, x-linked 0.167 1 3.23e-4 6.41e-4 ✓ sig.
46,xx sex reversal X-linked pituitary hormone deficiency with or without intellectual developmental disorder 0.167 1 3.23e-4 6.41e-4 ✓ sig.
46,xx ovotesticular disorder of sex development Panhypopituitarism, x-linked 0.143 1 3.87e-4 7.33e-4 ✓ sig.
46,xx ovotesticular disorder of sex development X-linked congenital generalized hypertrichosis 0.143 1 3.87e-4 7.33e-4 ✓ sig.
46,xx ovotesticular disorder of sex development X-linked pituitary hormone deficiency with or without intellectual developmental disorder 0.143 1 3.87e-4 7.33e-4 ✓ sig.
46,xx sex reversal Genetic panhypopituitarism 0.143 1 6.46e-4 1.09e-3 ✓ sig.
46,xx ovotesticular disorder of sex development Gametogenic failure 0.125 1 7.75e-4 1.25e-3 ✓ sig.
46,xx ovotesticular disorder of sex development Genetic panhypopituitarism 0.125 1 7.75e-4 1.25e-3 ✓ sig.