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 140

11 diseases · 25 shared-gene connections
11 Diseases
11 Unique genes
0.318 Avg. similarity score
Genitopatellar syndrome Most-connected disease (7 links)
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Disease Searched: Nicolaides-baraitser syndrome 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 ⇵
Genitopatellar syndrome 7 7 1
Sbbyss syndrome 7 7 1
Simpson syndrome 7 7 1
Blepharophimosis-intellectual disability syndrome 6 6 4
KAT6B-related disorders 6 6 1
Blepharophimosis syndrome 5 5 3
Multiple congenital anomalies 5 5 7
Ohdo syndrome, sbbys variant 4 4 1
Neurofacioskeletal syndrome with or without renal agenesis 1 1 1
Nicolaides-baraitser syndrome 1 1 1
Oculocerebrofacial syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KAT6B 8 / 11 Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome, Genitopatellar syndrome, KAT6B-related disorders and 4 more
HS2ST1 2 / 11 Multiple congenital anomalies, Neurofacioskeletal syndrome with or without renal agenesis
MED12 2 / 11 Blepharophimosis syndrome, Blepharophimosis-intellectual disability syndrome
SMARCA2 2 / 11 Blepharophimosis-intellectual disability syndrome, Nicolaides-baraitser syndrome
UBE3B 2 / 11 Blepharophimosis-intellectual disability syndrome, Oculocerebrofacial syndrome
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 ⇵
ATP-dependent chromatin remodeling
SMARCA2, TRRAP
 KEGG 2 / 117 18.7× 4.89e-3 3.60e-2 ✓ sig.
Cation-coupled Chloride cotransporters
SLC12A2
 Reactome 1 / 7 156× 6.40e-3 4.28e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1)
CDX2
 Reactome 1 / 14 78.0× 1.28e-2 6.57e-2
Virion - Lassa virus and SFTS virus
MYH10
 KEGG 1 / 17 64.2× 1.55e-2 7.39e-2
SUMOylation of transcription factors
FOXL2
 Reactome 1 / 18 60.7× 1.64e-2 7.63e-2
RHO GTPases activate PAKs
MYH10
 Reactome 1 / 23 47.5× 2.09e-2 8.78e-2
Glycosaminoglycan biosynthesis - heparan sulfate / heparin
HS2ST1
 KEGG 1 / 24 45.5× 2.18e-2 9.00e-2
HS-GAG biosynthesis
HS2ST1
 Reactome 1 / 30 36.4× 2.71e-2 1.02e-1
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
SMARCA2
 Reactome 1 / 38 28.7× 3.43e-2 1.17e-1
Vibrio cholerae infection
SLC12A2
 KEGG 1 / 51 21.4× 4.58e-2 1.37e-1
Transcriptional regulation of white adipocyte differentiation
MED12
 Reactome 1 / 67 16.3× 5.97e-2 1.60e-1
RMTs methylate histone arginines
SMARCA2
 Reactome 1 / 79 13.8× 7.01e-2 1.76e-1
Formation of the beta-catenin:TCF transactivating complex
TRRAP
 Reactome 1 / 88 12.4× 7.77e-2 1.87e-1
Salivary secretion
SLC12A2
 KEGG 1 / 93 11.7× 8.20e-2 1.92e-1
HATs acetylate histones
KAT6B
 Reactome 1 / 93 11.7× 8.20e-2 1.92e-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 DNA-templated transcription
MED12, KAT6B, FOXL2, SMARCA2, CDX2, TRRAP
 GO:0045893 6 / 778 13.1× 1.97e-6 1.50e-4 ✓ sig.
regulation of transcription by RNA polymerase II
MED12, KAT6B, FOXL2, SMARCA2, CDX2, TRRAP
 GO:0006357 6 / 1,602 6.4× 1.24e-4 3.62e-3 ✓ sig.
establishment or maintenance of epithelial cell apical/basal polarity
CDX2, FAT1
 GO:0045197 2 / 29 117× 1.27e-4 3.66e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
MED12, KAT6B, FOXL2, SMARCA2, CDX2
 GO:0045944 5 / 1,208 7.0× 3.72e-4 7.81e-3 ✓ sig.
establishment of epithelial cell apical/basal polarity involved in camera-type eye morphogenesis
FAT1
 GO:0003412 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
female somatic sex determination
FOXL2
 GO:0019101 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
granulosa cell differentiation
FOXL2
 GO:0060014 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
positive regulation of cell volume
SLC12A2
 GO:0045795 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
somatic stem cell population maintenance
MED12, CDX2
 GO:0035019 2 / 64 53.1× 6.23e-4 1.10e-2 ✓ sig.
regulation of DNA-templated transcription
KAT6B, FOXL2, SMARCA2, CDX2, TRRAP
 GO:0006355 5 / 1,454 5.8× 8.79e-4 1.36e-2 ✓ sig.
positive regulation of cell differentiation
SMARCA2, CDX2
 GO:0045597 2 / 83 40.9× 1.04e-3 1.51e-2 ✓ sig.
positive regulation of aspartate secretion
SLC12A2
 GO:1904450 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
inorganic cation import across plasma membrane
SLC12A2
 GO:0098659 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
inorganic anion import across plasma membrane
SLC12A2
 GO:0098658 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.
fourth ventricle development
MYH10
 GO:0021592 1 / 2 849× 1.18e-3 1.59e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Blepharophimosis syndrome Blepharophimosis-intellectual disability syndrome 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Genitopatellar syndrome Ohdo syndrome, sbbys variant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Sbbyss syndrome Simpson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ohdo syndrome, sbbys variant Sbbyss syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ohdo syndrome, sbbys variant Simpson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
KAT6B-related disorders Ohdo syndrome, sbbys variant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
KAT6B-related disorders Sbbyss syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
KAT6B-related disorders Simpson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Genitopatellar syndrome KAT6B-related disorders 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Genitopatellar syndrome Sbbyss syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Genitopatellar syndrome Simpson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Blepharophimosis syndrome KAT6B-related disorders 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blepharophimosis syndrome Sbbyss syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blepharophimosis syndrome Genitopatellar syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blepharophimosis syndrome Simpson syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome Sbbyss syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome Genitopatellar syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome Simpson syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome Nicolaides-baraitser syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blepharophimosis-intellectual disability syndrome Oculocerebrofacial syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Multiple congenital anomalies Simpson syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Genitopatellar syndrome Multiple congenital anomalies 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Multiple congenital anomalies Sbbyss syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
KAT6B-related disorders Multiple congenital anomalies 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Multiple congenital anomalies Neurofacioskeletal syndrome with or without renal agenesis 0.125 1 4.52e-4 8.26e-4 ✓ sig.