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 129

10 diseases · 17 shared-gene connections
10 Diseases
106 Unique genes
0.083 Avg. similarity score
Intellectual developmental disorder, x-linked Most-connected disease (8 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 ⇵
Intellectual developmental disorder, x-linked 8 8 89
X-linked intellectual disability 8 8 74
X-linked complex neurodevelopmental disorder 4 4 35
X-linked syndromic complex neurodevelopmental disorder 3 3 3
Hyperekplexia epilepsy syndrome 2 2 1
X-linked immunodeficiency with magnesium defect, epstein-barr virus infection and neoplasia 2 2 1
syndromic X-linked intellectual disability Nascimento type 2 2 1
syndromic X-linked intellectual disability Raymond type 2 2 1
syndromic X-linked intellectual disability Siderius type 2 2 1
intellectual disability, X-linked 106 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AP1S2 4 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability, X-linked syndromic complex neurodevelopmental disorder
AGTR2 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
ARHGEF9 3 / 10 Hyperekplexia epilepsy syndrome, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
ARX 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
CLCN4 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
CLIC2 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
CNKSR2 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
FRMPD4 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
FTSJ1 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
GRIA3 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
IL1RAPL1 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
IQSEC2 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
KDM5C 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
MAGT1 3 / 10 Intellectual developmental disorder, x-linked, X-linked immunodeficiency with magnesium defect, epstein-barr virus infection and neoplasia, X-linked intellectual disability
NEXMIF 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
PAK3 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
PHF8 3 / 10 Intellectual developmental disorder, x-linked, syndromic X-linked intellectual disability Siderius type, X-linked intellectual disability
PTCHD1 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
TFE3 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked syndromic complex neurodevelopmental disorder
THOC2 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
UBE2A 3 / 10 Intellectual developmental disorder, x-linked, syndromic X-linked intellectual disability Nascimento type, X-linked intellectual disability
UPF3B 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
USP27X 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
ZDHHC9 3 / 10 Intellectual developmental disorder, x-linked, syndromic X-linked intellectual disability Raymond type, X-linked intellectual disability
ZFX 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked syndromic complex neurodevelopmental disorder
ZNF711 3 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder, X-linked intellectual disability
ACSL4 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
AFF2 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ALG13 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ARHGEF6 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ATP6AP2 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ATRX 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
BRWD3 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
CASK 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
CUL4B 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
DDX3X 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
DLG3 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
DMD 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
FAM50A 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
FGD1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
GDI1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
HCFC1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
HNRNPH2 2 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder
HUWE1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
LAS1L 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
MECP2 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
MED12 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
MID2 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
NLGN4X 2 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder
NONO 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
OGT 2 / 10 Intellectual developmental disorder, x-linked, intellectual disability, X-linked 106
OPHN1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
PCDH19 2 / 10 X-linked complex neurodevelopmental disorder, X-linked intellectual disability
RAB39B 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
RBMX 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
RLIM 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
RPL10 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
RPS6KA3 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
SHROOM4 2 / 10 X-linked complex neurodevelopmental disorder, X-linked intellectual disability
SLC9A7 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
SLITRK2 2 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder
SMARCA1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
SMS 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
SOX3 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
STEEP1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
SYN1 2 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder
SYP 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
TAF1 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
TSPAN7 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
USP9X 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ZDHHC15 2 / 10 Intellectual developmental disorder, x-linked, X-linked complex neurodevelopmental disorder
ZNF41 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ZNF674 2 / 10 Intellectual developmental disorder, x-linked, X-linked intellectual disability
ZNF81 2 / 10 Intellectual developmental disorder, x-linked, X-linked 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 ⇵
Neurexins and neuroligins
NLGN4X, DLG3, CASK, NLGN3
 Reactome 4 / 32 14.2× 1.70e-4 3.45e-3 ✓ sig.
Sodium/Proton exchangers
SLC9A7, SLC9A6
 Reactome 2 / 9 25.2× 2.67e-3 2.83e-2 ✓ sig.
Processing of Capped Intron-Containing Pre-mRNA
RBMX, HNRNPH1, HNRNPH2
 Reactome 3 / 37 9.2× 4.18e-3 3.88e-2 ✓ sig.
mRNA Splicing - Major Pathway
CSTF2, RBMX, UPF3B, HNRNPH1, HNRNPH2, PQBP1
 Reactome 6 / 183 3.7× 5.59e-3 4.71e-2 ✓ sig.
Rho GTPase cycle
ARHGEF9, ARHGEF6, GDI1, FGD1, OPHN1
 Reactome 5 / 138 4.1× 7.47e-3 5.69e-2
Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH)
SLC9A6
 Reactome 1 / 1 113× 8.83e-3 6.36e-2
Defective MAOA causes Brunner syndrome (BRUNS)
MAOA
 Reactome 1 / 1 113× 8.83e-3 6.36e-2
Loss of MECP2 binding ability to 5hmC-DNA
MECP2
 Reactome 1 / 1 113× 8.83e-3 6.36e-2
Defective SLC35A2 causes congenital disorder of glycosylation 2M (CDG2M)
SLC35A2
 Reactome 1 / 1 113× 8.83e-3 6.36e-2
Trafficking of GluR2-containing AMPA receptors
TSPAN7, GRIA3
 Reactome 2 / 17 13.3× 9.63e-3 6.71e-2
NRAGE signals death through JNK
ARHGEF9, ARHGEF6, FGD1
 Reactome 3 / 55 6.2× 1.26e-2 7.84e-2
Receptor-type tyrosine-protein phosphatases
SLITRK2, IL1RAPL1
 Reactome 2 / 20 11.3× 1.32e-2 8.07e-2
mRNA 3'-end processing
CSTF2, THOC2, UPF3B
 Reactome 3 / 58 5.9× 1.45e-2 8.54e-2
Synaptic adhesion-like molecules
DLG3, GRIA3
 Reactome 2 / 21 10.8× 1.45e-2 8.54e-2
Unblocking of NMDA receptors, glutamate binding and activation
DLG3, GRIA3
 Reactome 2 / 22 10.3× 1.59e-2 9.02e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
modulation of chemical synaptic transmission
NLGN4X, IQSEC2, SYN1, SYP, GLRA2, GRIA3, NLGN3
 GO:0050804 7 / 121 10.2× 5.75e-6 3.35e-4 ✓ sig.
presynaptic membrane assembly
NLGN4X, IL1RAPL1, NLGN3
 GO:0097105 3 / 9 58.8× 1.45e-5 6.99e-4 ✓ sig.
chromatin organization
HCFC1, SMARCA1, OGT, TAF1, FAM50A, KDM5C, UBE2A, PHF8, PHIP, HDAC8, ATRX
 GO:0006325 11 / 449 4.3× 4.87e-5 1.76e-3 ✓ sig.
synapse organization
NLGN4X, PAK3, SYN1, RAB39B, NLGN3
 GO:0050808 5 / 72 12.2× 5.53e-5 1.94e-3 ✓ sig.
brain development
SMARCA1, AFF2, MECP2, UPF3B, PHF8, SOX3, AGTR2, SHROOM4
 GO:0007420 8 / 244 5.8× 7.56e-5 2.46e-3 ✓ sig.
regulation of RNA splicing
AFF2, FAM50A, HNRNPH1, HNRNPH2, PQBP1
 GO:0043484 5 / 78 11.3× 8.12e-5 2.59e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
HCFC1, SMARCA1, OGT, RPS6KA3, ARX, ZNF711, RBMX, MECP2, TAF1, ZFX, MED12, PHF8
 GO:0045944 18 / 1,208 2.6× 1.44e-4 3.98e-3 ✓ sig.
neuron differentiation
NLGN4X, SMARCA1, IL1RAPL1, ACSL4, MECP2, OPHN1, SOX3
 GO:0030182 7 / 222 5.6× 2.74e-4 6.29e-3 ✓ sig.
biogenic amine metabolic process
MECP2, MAOA
 GO:0006576 2 / 5 70.5× 3.15e-4 6.96e-3 ✓ sig.
social behavior
NLGN4X, MECP2, PTCHD1, NLGN3
 GO:0035176 4 / 58 12.2× 3.28e-4 7.13e-3 ✓ sig.
chromatin remodeling
HCFC1, HUWE1, SMARCA1, TAF1, KDM5C, UBE2A, PHF8, ATRX
 GO:0006338 8 / 320 4.4× 4.77e-4 9.29e-3 ✓ sig.
learning
NLGN4X, FGF13, MECP2, NLGN3
 GO:0007612 4 / 64 11.0× 4.78e-4 9.31e-3 ✓ sig.
positive regulation of synapse assembly
IQSEC2, SLITRK2, IL1RAPL1, NLGN3
 GO:0051965 4 / 68 10.4× 6.03e-4 1.09e-2 ✓ sig.
ubiquitin-dependent protein catabolic process
HUWE1, KLHL15, TAF1, CUL4B, UBE2A, ZDHHC9, RLIM
 GO:0006511 7 / 257 4.8× 6.57e-4 1.15e-2 ✓ sig.
neuron development
THOC2, ARX, SYN1, DMD
 GO:0048666 4 / 77 9.2× 9.63e-4 1.47e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Intellectual developmental disorder, x-linked X-linked intellectual disability 0.624 63 2.95e-142 5.42e-140 ✓ sig.
Intellectual developmental disorder, x-linked X-linked complex neurodevelopmental disorder 0.263 26 7.74e-53 4.47e-51 ✓ sig.
X-linked complex neurodevelopmental disorder X-linked intellectual disability 0.250 22 4.43e-44 2.16e-42 ✓ sig.
X-linked complex neurodevelopmental disorder X-linked syndromic complex neurodevelopmental disorder 0.083 3 1.08e-8 9.10e-8 ✓ sig.
Intellectual developmental disorder, x-linked X-linked syndromic complex neurodevelopmental disorder 0.033 3 1.87e-7 1.31e-6 ✓ sig.
Hyperekplexia epilepsy syndrome X-linked complex neurodevelopmental disorder 0.028 1 2.27e-3 3.18e-3 ✓ sig.
Hyperekplexia epilepsy syndrome X-linked intellectual disability 0.013 1 4.81e-3 5.92e-3 ✓ sig.
syndromic X-linked intellectual disability Nascimento type X-linked intellectual disability 0.013 1 4.81e-3 5.92e-3 ✓ sig.
syndromic X-linked intellectual disability Raymond type X-linked intellectual disability 0.013 1 4.81e-3 5.92e-3 ✓ sig.
syndromic X-linked intellectual disability Siderius type X-linked intellectual disability 0.013 1 4.81e-3 5.92e-3 ✓ sig.
X-linked immunodeficiency with magnesium defect, epstein-barr virus infection and neoplasia X-linked intellectual disability 0.013 1 4.81e-3 5.92e-3 ✓ sig.
Intellectual developmental disorder, x-linked syndromic X-linked intellectual disability Raymond type 0.011 1 5.78e-3 7.00e-3 ✓ sig.
Intellectual developmental disorder, x-linked X-linked immunodeficiency with magnesium defect, epstein-barr virus infection and neoplasia 0.011 1 5.78e-3 7.00e-3 ✓ sig.
Intellectual developmental disorder, x-linked syndromic X-linked intellectual disability Siderius type 0.011 1 5.78e-3 7.00e-3 ✓ sig.
Intellectual developmental disorder, x-linked syndromic X-linked intellectual disability Nascimento type 0.011 1 5.78e-3 7.00e-3 ✓ sig.
Intellectual developmental disorder, x-linked intellectual disability, X-linked 106 0.011 1 5.78e-3 7.00e-3 ✓ sig.
X-linked intellectual disability X-linked syndromic complex neurodevelopmental disorder 0.013 1 1.43e-2 1.59e-2 ✓ sig.