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Cluster 569

5 diseases · 9 shared-gene connections

5 Diseases

3 Unique genes

0.389 Avg. similarity score

Autism, intellectual disability, basal ganglia dysfunction and epilepsy Most-connected disease (4 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.

Autism, intellectual disability, basal ganglia dysfunction and epilepsy Mental retardation, autosomal dominant 24 Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures Intellectual developmental disorder seizures extrapyramidal Vulto-van silfhout-de vries syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Autism, intellectual disability, basal ganglia dysfunction and epilepsy	4	4	1
Mental retardation, autosomal dominant 24	4	4	1
Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures	4	4	1
Intellectual developmental disorder seizures extrapyramidal	3	3	2
Vulto-van silfhout-de vries syndrome	3	3	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
DEAF1	5 / 5	Autism, intellectual disability, basal ganglia dysfunction and epilepsy, Intellectual developmental disorder seizures extrapyramidal, Mental retardation, autosomal dominant 24, Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures and 1 more

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 ⇵
RHO GTPases activate CIT DLG4	Reactome	1 / 8	500×	2.00e-3	1.90e-2 ✓ sig.
Activation of Ca-permeable Kainate Receptor DLG4	Reactome	1 / 12	334×	2.99e-3	2.54e-2 ✓ sig.
LGI-ADAM interactions DLG4	Reactome	1 / 14	286×	3.49e-3	2.83e-2 ✓ sig.
Trafficking of AMPA receptors DLG4	Reactome	1 / 17	235×	4.24e-3	3.26e-2 ✓ sig.
Apoptotic cleavage of cellular proteins SATB1	Reactome	1 / 18	222×	4.49e-3	3.39e-2 ✓ sig.
Synaptic adhesion-like molecules DLG4	Reactome	1 / 21	191×	5.24e-3	3.76e-2 ✓ sig.
Unblocking of NMDA receptors, glutamate binding and activation DLG4	Reactome	1 / 22	182×	5.49e-3	3.87e-2 ✓ sig.
Neurexins and neuroligins DLG4	Reactome	1 / 32	125×	7.97e-3	4.94e-2 ✓ sig.
Cocaine addiction DLG4	KEGG	1 / 49	81.7×	1.22e-2	6.42e-2
SUMOylation of chromatin organization proteins SATB1	Reactome	1 / 70	57.2×	1.74e-2	7.89e-2
Glutamatergic synapse DLG4	KEGG	1 / 116	34.5×	2.87e-2	1.06e-1
RAF/MAP kinase cascade DLG4	Reactome	1 / 124	32.3×	3.07e-2	1.10e-1
Hippo signaling pathway DLG4	KEGG	1 / 157	25.5×	3.87e-2	1.25e-1
Huntington disease DLG4	KEGG	1 / 308	13.0×	7.50e-2	1.83e-1
Pathways of neurodegeneration - multiple diseases DLG4	KEGG	1 / 480	8.3×	1.15e-1	2.35e-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 ⇵
regulation of grooming behavior DLG4	GO:2000821	1 / 3	2,076×	4.82e-4	9.24e-3 ✓ sig.
AMPA glutamate receptor clustering DLG4	GO:0097113	1 / 5	1,246×	8.03e-4	1.28e-2 ✓ sig.
regulation of mammary gland epithelial cell proliferation DEAF1	GO:0033599	1 / 5	1,246×	8.03e-4	1.28e-2 ✓ sig.
NMDA selective glutamate receptor signaling pathway DLG4	GO:0098989	1 / 6	1,038×	9.63e-4	1.42e-2 ✓ sig.
positive regulation of neuron projection arborization DLG4	GO:0150012	1 / 8	779×	1.28e-3	1.67e-2 ✓ sig.
receptor localization to synapse DLG4	GO:0097120	1 / 9	692×	1.44e-3	1.79e-2 ✓ sig.
synaptic vesicle maturation DLG4	GO:0016188	1 / 9	692×	1.44e-3	1.79e-2 ✓ sig.
cellular response to potassium ion DLG4	GO:0035865	1 / 14	445×	2.25e-3	2.24e-2 ✓ sig.
negative regulation of receptor internalization DLG4	GO:0002091	1 / 15	415×	2.41e-3	2.32e-2 ✓ sig.
locomotory exploration behavior DLG4	GO:0035641	1 / 16	389×	2.57e-3	2.40e-2 ✓ sig.
regulation of long-term neuronal synaptic plasticity DLG4	GO:0048169	1 / 18	346×	2.89e-3	2.55e-2 ✓ sig.
positive regulation of synaptic transmission DLG4	GO:0050806	1 / 18	346×	2.89e-3	2.55e-2 ✓ sig.
dendritic spine morphogenesis DLG4	GO:0060997	1 / 18	346×	2.89e-3	2.55e-2 ✓ sig.
protein localization to synapse DLG4	GO:0035418	1 / 19	328×	3.05e-3	2.62e-2 ✓ sig.
vocalization behavior DLG4	GO:0071625	1 / 19	328×	3.05e-3	2.62e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Autism, intellectual disability, basal ganglia dysfunction and epilepsy	Mental retardation, autosomal dominant 24	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Autism, intellectual disability, basal ganglia dysfunction and epilepsy	Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 24	Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Autism, intellectual disability, basal ganglia dysfunction and epilepsy	Intellectual developmental disorder seizures extrapyramidal	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Autism, intellectual disability, basal ganglia dysfunction and epilepsy	Vulto-van silfhout-de vries syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Intellectual developmental disorder seizures extrapyramidal	Mental retardation, autosomal dominant 24	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Intellectual developmental disorder seizures extrapyramidal	Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Mental retardation, autosomal dominant 24	Vulto-van silfhout-de vries syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizures	Vulto-van silfhout-de vries syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.

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