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 223

9 diseases · 24 shared-gene connections
9 Diseases
5 Unique genes
0.415 Avg. similarity score
Corpus callosum agenesis with abnormal genitalia Most-connected disease (7 links)
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Disease Searched: Proud 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 ⇵
Corpus callosum agenesis with abnormal genitalia 7 7 1
Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 7 7 1
X-linked spasticity-intellectual disability-epilepsy syndrome 7 7 1
Hydranencephaly with abnormal genitalia 6 6 1
Proud syndrome 6 6 1
Epileptic encephalopathy early infantile type 1 5 5 1
Lissencephaly, x-linked 5 5 2
Arachnoid cysts 4 4 4
Ciliary dyskinesia, primary, 42 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ARX 8 / 9 Arachnoid cysts, Corpus callosum agenesis with abnormal genitalia, Epileptic encephalopathy early infantile type 1, Hydranencephaly with abnormal genitalia and 4 more
MCIDAS 2 / 9 Arachnoid cysts, Ciliary dyskinesia, primary, 42
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 ⇵
Molybdenum cofactor biosynthesis
GPHN
 Reactome 1 / 6 400× 2.50e-3 2.23e-2 ✓ sig.
Folate biosynthesis
GPHN
 KEGG 1 / 28 85.8× 1.16e-2 6.22e-2
GABAergic synapse
GPHN
 KEGG 1 / 89 27.0× 3.65e-2 1.21e-1
Biosynthesis of cofactors
GPHN
 KEGG 1 / 154 15.6× 6.25e-2 1.64e-1
Hippo signaling pathway
PALS1
 KEGG 1 / 157 15.3× 6.37e-2 1.66e-1
Tight junction
PALS1
 KEGG 1 / 170 14.1× 6.88e-2 1.74e-1
Human papillomavirus infection
PALS1
 KEGG 1 / 333 7.2× 1.31e-1 2.54e-1
Metabolic pathways
GPHN
 KEGG 1 / 1,563 1.5× 5.02e-1 6.20e-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 ⇵
glycine receptor clustering
GPHN
 GO:0072579 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
protein localization to myelin sheath abaxonal region
PALS1
 GO:0035750 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
neuron migration
ARX, DCX
 GO:0001764 2 / 132 56.6× 4.88e-4 9.34e-3 ✓ sig.
establishment of synaptic specificity at neuromuscular junction
GPHN
 GO:0007529 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
embryonic olfactory bulb interneuron precursor migration
ARX
 GO:0021831 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
establishment or maintenance of polarity of embryonic epithelium
PALS1
 GO:0016332 1 / 3 1,246× 8.03e-4 1.28e-2 ✓ sig.
cerebral cortex tangential migration
ARX
 GO:0021800 1 / 4 934× 1.07e-3 1.51e-2 ✓ sig.
epithelial cell fate commitment
ARX
 GO:0072148 1 / 4 934× 1.07e-3 1.51e-2 ✓ sig.
globus pallidus development
ARX
 GO:0021759 1 / 4 934× 1.07e-3 1.51e-2 ✓ sig.
molybdopterin cofactor biosynthetic process
GPHN
 GO:0032324 1 / 4 934× 1.07e-3 1.51e-2 ✓ sig.
lipid digestion
ARX
 GO:0044241 1 / 5 747× 1.34e-3 1.71e-2 ✓ sig.
multi-ciliated epithelial cell differentiation
MCIDAS
 GO:1903251 1 / 6 623× 1.60e-3 1.88e-2 ✓ sig.
cerebral cortex GABAergic interneuron migration
ARX
 GO:0021853 1 / 6 623× 1.60e-3 1.88e-2 ✓ sig.
gamma-aminobutyric acid receptor clustering
GPHN
 GO:0097112 1 / 6 623× 1.60e-3 1.88e-2 ✓ sig.
Mo-molybdopterin cofactor biosynthetic process
GPHN
 GO:0006777 1 / 6 623× 1.60e-3 1.88e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Epileptic encephalopathy early infantile type 1 Hydranencephaly with abnormal genitalia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Proud syndrome X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability Proud syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hydranencephaly with abnormal genitalia Proud syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hydranencephaly with abnormal genitalia Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hydranencephaly with abnormal genitalia X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy early infantile type 1 Proud syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy early infantile type 1 Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy early infantile type 1 X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Epileptic encephalopathy early infantile type 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Hydranencephaly with abnormal genitalia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Proud syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Lissencephaly, x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lissencephaly, x-linked X-linked spasticity-intellectual disability-epilepsy syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lissencephaly, x-linked Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lissencephaly, x-linked Proud syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hydranencephaly with abnormal genitalia Lissencephaly, x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arachnoid cysts Corpus callosum agenesis with abnormal genitalia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Arachnoid cysts Ciliary dyskinesia, primary, 42 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Arachnoid cysts Neurodevelopmental spectrum including lissencephaly with genital anomalies and epilepsy to non-syndromic intellectual disability 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Arachnoid cysts X-linked spasticity-intellectual disability-epilepsy syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.