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 286

6 diseases · 7 shared-gene connections
6 Diseases
36 Unique genes
0.118 Avg. similarity score
syndromic intellectual disability Most-connected disease (5 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 ⇵
syndromic intellectual disability 5 5 36
Intellectual disability with craniofacial anomalies and cardiac defects 3 3 2
Arboleda-tham syndrome 2 2 1
Intellectual disability with craniofacial dysmorphism and macrocephaly 2 2 1
Congenital heart defect, intellectual disability, facial dysmorphism syndrome 1 1 1
Diets-jongmans syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
H1-4 3 / 6 Intellectual disability with craniofacial anomalies and cardiac defects, Intellectual disability with craniofacial dysmorphism and macrocephaly, syndromic intellectual disability
KAT6A 3 / 6 Arboleda-tham syndrome, Intellectual disability with craniofacial anomalies and cardiac defects, syndromic intellectual disability
CDK13 2 / 6 Congenital heart defect, intellectual disability, facial dysmorphism syndrome, syndromic intellectual disability
KDM3B 2 / 6 Diets-jongmans syndrome, syndromic intellectual disability
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 ⇵
DCC mediated attractive signaling
RAC1, TRIO
 Reactome 2 / 11 60.7× 4.72e-4 7.63e-3 ✓ sig.
Signal transduction by L1
CSNK2A1, RAC1
 Reactome 2 / 21 31.8× 1.77e-3 2.09e-2 ✓ sig.
Polycomb repressive complex
AUTS2, ASXL2, ASXL3
 KEGG 3 / 83 12.1× 1.93e-3 2.22e-2 ✓ sig.
Regulation of TP53 Activity through Acetylation
KAT6A, CHD4
 Reactome 2 / 23 29.0× 2.12e-3 2.38e-2 ✓ sig.
Processing of Capped Intron-Containing Pre-mRNA
HNRNPR, HNRNPH1
 Reactome 2 / 37 18.0× 5.45e-3 4.63e-2 ✓ sig.
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
AUTS2, CSNK2A1
 Reactome 2 / 38 17.6× 5.74e-3 4.80e-2 ✓ sig.
HDMs demethylate histones
KDM3B, KDM6B
 Reactome 2 / 50 13.3× 9.78e-3 6.77e-2
NRAGE signals death through JNK
RAC1, TRIO
 Reactome 2 / 55 12.1× 1.17e-2 7.55e-2
NTRK2 activates RAC1
RAC1
 Reactome 1 / 5 66.7× 1.49e-2 8.66e-2
Lysine degradation
KMT2C, NSD2
 KEGG 2 / 63 10.6× 1.52e-2 8.77e-2
Transcriptional regulation of white adipocyte differentiation
MED13L, MED23
 Reactome 2 / 67 10.0× 1.71e-2 9.45e-2
mRNA Splicing - Major Pathway
HNRNPR, PUF60, HNRNPH1
 Reactome 3 / 183 5.5× 1.72e-2 9.47e-2
PKMTs methylate histone lysines
KMT2C, NSD2
 Reactome 2 / 71 9.4× 1.91e-2 1.00e-1
Condensation of Prometaphase Chromosomes
CSNK2A1
 Reactome 1 / 8 41.7× 2.37e-2 1.13e-1
Sema4D mediated inhibition of cell attachment and migration
RAC1
 Reactome 1 / 8 41.7× 2.37e-2 1.13e-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 ⇵
chromatin organization
KAT6A, H1-4, KDM3B, BPTF, CTCF, KDM6B, KMT2C, CHD4, BRD4, NSD2
 GO:0006325 10 / 449 11.6× 8.43e-9 1.48e-6 ✓ sig.
positive regulation of transcription by RNA polymerase II
CDK13, AUTS2, ASXL2, ASXL3, BPTF, CTCF, KDM6B, KMT2C, HOXA1, MEIS2, MED13L, BRD4
 GO:0045944 12 / 1,208 5.2× 1.48e-6 1.13e-4 ✓ sig.
chromatin remodeling
KDM3B, BPTF, KDM6B, KMT2C, CHD4, BRD4, NSD2
 GO:0006338 7 / 320 11.4× 2.20e-6 1.56e-4 ✓ sig.
regulation of DNA-templated transcription
KAT6A, ASXL2, ASXL3, BPTF, CTCF, KMT2C, HOXA1, MEIS2, BRD4, NSD2, MED23
 GO:0006355 11 / 1,454 3.9× 5.92e-5 2.04e-3 ✓ sig.
N-terminal protein amino acid acetylation
NAA15, NAA20
 GO:0006474 2 / 8 130× 1.00e-4 3.03e-3 ✓ sig.
positive regulation of transcription elongation by RNA polymerase II
CDK13, BRD4, MED23
 GO:0032968 3 / 57 27.3× 1.79e-4 4.67e-3 ✓ sig.
aggrephagy
CSNK2A1, WDFY3
 GO:0035973 2 / 15 69.2× 3.73e-4 7.80e-3 ✓ sig.
regulation of transcription by RNA polymerase II
KAT6A, H1-4, KDM3B, BPTF, CSNK2A1, CTCF, HOXA1, MED13L, BRD4, MED23
 GO:0006357 10 / 1,602 3.2× 6.65e-4 1.16e-2 ✓ sig.
regulation of stem cell differentiation
NSUN2, CHD4
 GO:2000736 2 / 23 45.1× 8.90e-4 1.40e-2 ✓ sig.
regulation of actin cytoskeleton organization
RAC1, TAOK1, NAA20
 GO:0032956 3 / 104 15.0× 1.05e-3 1.55e-2 ✓ sig.
execution phase of apoptosis
CSNK2A1, TAOK1
 GO:0097194 2 / 25 41.5× 1.05e-3 1.56e-2 ✓ sig.
alternative mRNA splicing, via spliceosome
CDK13, PUF60
 GO:0000380 2 / 25 41.5× 1.05e-3 1.56e-2 ✓ sig.
mRNA processing
CDK13, HNRNPR, PUF60, NSUN2, HNRNPH1
 GO:0006397 5 / 410 6.3× 1.07e-3 1.57e-2 ✓ sig.
DNA methylation-dependent constitutive heterochromatin formation
CTCF, PPM1D
 GO:0006346 2 / 26 39.9× 1.14e-3 1.64e-2 ✓ sig.
positive regulation of lamellipodium assembly
AUTS2, RAC1
 GO:0010592 2 / 28 37.1× 1.32e-3 1.79e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Intellectual disability with craniofacial anomalies and cardiac defects syndromic intellectual disability 0.054 2 5.31e-6 2.90e-5 ✓ sig.
Arboleda-tham syndrome Intellectual disability with craniofacial anomalies and cardiac defects 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Intellectual disability with craniofacial anomalies and cardiac defects Intellectual disability with craniofacial dysmorphism and macrocephaly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Arboleda-tham syndrome syndromic intellectual disability 0.027 1 2.34e-3 3.23e-3 ✓ sig.
Congenital heart defect, intellectual disability, facial dysmorphism syndrome syndromic intellectual disability 0.027 1 2.34e-3 3.23e-3 ✓ sig.
Diets-jongmans syndrome syndromic intellectual disability 0.027 1 2.34e-3 3.23e-3 ✓ sig.
Intellectual disability with craniofacial dysmorphism and macrocephaly syndromic intellectual disability 0.027 1 2.34e-3 3.23e-3 ✓ sig.