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Cluster 329

6 diseases · 8 shared-gene connections

6 Diseases

14 Unique genes

0.142 Avg. similarity score

Partington syndrome Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Partington syndrome X-linked syndromic intellectual disability Intellectual developmental disorder microcephaly cerebellar X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability X-linked myopathy with excessive autophagy intellectual disability, X-linked 107

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Partington syndrome	5	5	14
X-linked syndromic intellectual disability	4	4	8
Intellectual developmental disorder microcephaly cerebellar	2	2	1
X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability	2	2	1
X-linked myopathy with excessive autophagy	2	2	1
intellectual disability, X-linked 107	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
CASK	3 / 6	Intellectual developmental disorder microcephaly cerebellar, Partington syndrome, X-linked syndromic intellectual disability
RPL10	3 / 6	Partington syndrome, X-linked myopathy with excessive autophagy, X-linked syndromic intellectual disability
USP9X	3 / 6	Partington syndrome, X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability, X-linked syndromic intellectual disability
BRWD3	2 / 6	Partington syndrome, X-linked syndromic intellectual disability
DDX3X	2 / 6	Partington syndrome, X-linked syndromic intellectual disability
LAS1L	2 / 6	Partington syndrome, X-linked syndromic intellectual disability
NONO	2 / 6	Partington syndrome, X-linked syndromic intellectual disability
STEEP1	2 / 6	intellectual disability, X-linked 107, Partington syndrome
ZC4H2	2 / 6	Partington syndrome, X-linked 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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
Nef mediated downregulation of MHC class I complex cell surface expression AP1S2	Reactome	1 / 10	85.8×	1.16e-2	7.50e-2
CD28 dependent Vav1 pathway PAK3	Reactome	1 / 12	71.5×	1.39e-2	8.31e-2
Sema3A PAK dependent Axon repulsion PAK3	Reactome	1 / 15	57.2×	1.74e-2	9.50e-2
Major pathway of rRNA processing in the nucleolus and cytosol LAS1L, RPL10	Reactome	2 / 184	9.3×	1.88e-2	9.94e-2
Ephrin signaling PAK3	Reactome	1 / 19	45.2×	2.19e-2	1.08e-1
CD209 (DC-SIGN) signaling PAK3	Reactome	1 / 21	40.9×	2.42e-2	1.15e-1
Human immunodeficiency virus 1 infection AP1S2, PAK3	KEGG	2 / 213	8.1×	2.48e-2	1.16e-1
Downregulation of SMAD2/3:SMAD4 transcriptional activity USP9X	Reactome	1 / 22	39.0×	2.54e-2	1.17e-1
RHO GTPases activate PAKs PAK3	Reactome	1 / 23	37.3×	2.65e-2	1.20e-1
Dopamine Neurotransmitter Release Cycle CASK	Reactome	1 / 23	37.3×	2.65e-2	1.20e-1
VEGFR2 mediated vascular permeability PAK3	Reactome	1 / 29	29.6×	3.33e-2	1.37e-1
Synthesis of active ubiquitin: roles of E1 and E2 enzymes USP9X	Reactome	1 / 30	28.6×	3.44e-2	1.39e-1
Generation of second messenger molecules PAK3	Reactome	1 / 31	27.7×	3.56e-2	1.42e-1
Neurexins and neuroligins CASK	Reactome	1 / 32	26.8×	3.67e-2	1.44e-1
Lysosome Vesicle Biogenesis AP1S2	Reactome	1 / 35	24.5×	4.01e-2	1.52e-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 ⇵
rhythmic process KDM5C, NONO, USP9X	GO:0048511	3 / 148	27.1×	1.66e-4	4.42e-3 ✓ sig.
positive regulation of type I interferon production DDX3X, STEEP1	GO:0032481	2 / 54	49.4×	7.29e-4	1.23e-2 ✓ sig.
regulation of circadian rhythm NONO, USP9X	GO:0042752	2 / 66	40.4×	1.09e-3	1.59e-2 ✓ sig.
embryonic olfactory bulb interneuron precursor migration ARX	GO:0021831	1 / 2	667×	1.50e-3	1.91e-2 ✓ sig.
negative regulation of cellular response to growth factor stimulus CASK	GO:0090288	1 / 2	667×	1.50e-3	1.91e-2 ✓ sig.
positive regulation of toll-like receptor 8 signaling pathway DDX3X	GO:0034161	1 / 3	445×	2.25e-3	2.41e-2 ✓ sig.
chromosome segregation DDX3X, USP9X	GO:0007059	2 / 110	24.3×	2.98e-3	2.82e-2 ✓ sig.
cerebral cortex tangential migration ARX	GO:0021800	1 / 4	334×	2.99e-3	2.82e-2 ✓ sig.
positive regulation of translation in response to endoplasmic reticulum stress DDX3X	GO:0036493	1 / 4	334×	2.99e-3	2.82e-2 ✓ sig.
epithelial cell fate commitment ARX	GO:0072148	1 / 4	334×	2.99e-3	2.82e-2 ✓ sig.
regulation of transcription regulatory region DNA binding ZC4H2	GO:2000677	1 / 4	334×	2.99e-3	2.82e-2 ✓ sig.
globus pallidus development ARX	GO:0021759	1 / 4	334×	2.99e-3	2.82e-2 ✓ sig.
cytosolic ribosome assembly DDX3X	GO:0042256	1 / 5	267×	3.74e-3	3.18e-2 ✓ sig.
lipid digestion ARX	GO:0044241	1 / 5	267×	3.74e-3	3.18e-2 ✓ sig.
noradrenergic neuron development ZC4H2	GO:0003358	1 / 5	267×	3.74e-3	3.18e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Partington syndrome	X-linked syndromic intellectual disability	0.533	8	3.84e-26	1.05e-24 ✓ sig.
Intellectual developmental disorder microcephaly cerebellar	X-linked syndromic intellectual disability	0.111	1	5.20e-4	1.04e-3 ✓ sig.
X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability	X-linked syndromic intellectual disability	0.111	1	5.20e-4	1.04e-3 ✓ sig.
X-linked myopathy with excessive autophagy	X-linked syndromic intellectual disability	0.111	1	5.20e-4	1.04e-3 ✓ sig.
Intellectual developmental disorder microcephaly cerebellar	Partington syndrome	0.067	1	9.09e-4	1.56e-3 ✓ sig.
intellectual disability, X-linked 107	Partington syndrome	0.067	1	9.09e-4	1.56e-3 ✓ sig.
Partington syndrome	X-linked female restricted facial dysmorphism, short stature, choanal atresia, intellectual disability	0.067	1	9.09e-4	1.56e-3 ✓ sig.
Partington syndrome	X-linked myopathy with excessive autophagy	0.067	1	9.09e-4	1.56e-3 ✓ sig.

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