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 255

7 diseases · 14 shared-gene connections
7 Diseases
8 Unique genes
0.294 Avg. similarity score
Corpus callosum agenesis with abnormal genitalia 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 ⇵
Corpus callosum agenesis with abnormal genitalia 5 5 1
X-linked lissencephaly 5 5 1
X-linked spasticity-intellectual disability-epilepsy syndrome 5 5 1
Arachnoid cysts 4 4 3
Lissencephaly, x-linked 4 4 2
Periventricular heterotopia 4 4 5
Benign mesial temporal lobe epilepsy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ARX 6 / 7 Arachnoid cysts, Corpus callosum agenesis with abnormal genitalia, Lissencephaly, x-linked, Periventricular heterotopia and 2 more
CPA6 2 / 7 Benign mesial temporal lobe epilepsy, Periventricular heterotopia
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 / 6 250× 3.99e-3 3.77e-2 ✓ sig.
Spliceosome
DHX15, DHX16
 KEGG 2 / 162 18.5× 4.80e-3 4.27e-2 ✓ sig.
mRNA Splicing - Major Pathway
DHX15, DHX16
 Reactome 2 / 183 16.4× 6.09e-3 4.98e-2 ✓ sig.
VxPx cargo-targeting to cilium
PKD1
 Reactome 1 / 21 71.5× 1.39e-2 8.31e-2
Folate biosynthesis
GPHN
 KEGG 1 / 28 53.6× 1.85e-2 9.85e-2
GABAergic synapse
GPHN
 KEGG 1 / 89 16.9× 5.78e-2 1.85e-1
Biosynthesis of cofactors
GPHN
 KEGG 1 / 154 9.7× 9.81e-2 2.45e-1
Hippo signaling pathway
PALS1
 KEGG 1 / 157 9.6× 9.99e-2 2.48e-1
Tight junction
PALS1
 KEGG 1 / 170 8.8× 1.08e-1 2.59e-1
Human papillomavirus infection
PALS1
 KEGG 1 / 333 4.5× 2.01e-1 3.66e-1
Metabolic pathways
GPHN
 KEGG 1 / 1,563 1.0× 6.72e-1 7.87e-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 2,336× 4.28e-4 8.59e-3 ✓ sig.
protein localization to myelin sheath abaxonal region
PALS1
 GO:0035750 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
metanephric distal tubule morphogenesis
PKD1
 GO:0072287 1 / 1 2,336× 4.28e-4 8.59e-3 ✓ sig.
antiviral innate immune response
DHX15, DHX16
 GO:0140374 2 / 79 59.1× 4.86e-4 9.37e-3 ✓ sig.
establishment of synaptic specificity at neuromuscular junction
GPHN
 GO:0007529 1 / 2 1,168× 8.56e-4 1.36e-2 ✓ sig.
embryonic olfactory bulb interneuron precursor migration
ARX
 GO:0021831 1 / 2 1,168× 8.56e-4 1.36e-2 ✓ sig.
nitrogen cycle metabolic process
PKD1
 GO:0071941 1 / 2 1,168× 8.56e-4 1.36e-2 ✓ sig.
establishment or maintenance of polarity of embryonic epithelium
PALS1
 GO:0016332 1 / 3 779× 1.28e-3 1.75e-2 ✓ sig.
lymph vessel morphogenesis
PKD1
 GO:0036303 1 / 3 779× 1.28e-3 1.75e-2 ✓ sig.
metanephric proximal tubule development
PKD1
 GO:0072237 1 / 3 779× 1.28e-3 1.75e-2 ✓ sig.
neuron migration
ARX, DCX
 GO:0001764 2 / 132 35.4× 1.35e-3 1.81e-2 ✓ sig.
cerebral cortex tangential migration
ARX
 GO:0021800 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.
epithelial cell fate commitment
ARX
 GO:0072148 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.
globus pallidus development
ARX
 GO:0021759 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.
molybdopterin cofactor biosynthetic process
GPHN
 GO:0032324 1 / 4 584× 1.71e-3 2.07e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Corpus callosum agenesis with abnormal genitalia X-linked lissencephaly 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
X-linked lissencephaly X-linked spasticity-intellectual disability-epilepsy syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Lissencephaly, x-linked 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Lissencephaly, x-linked X-linked lissencephaly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Lissencephaly, x-linked X-linked spasticity-intellectual disability-epilepsy syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Arachnoid cysts Corpus callosum agenesis with abnormal genitalia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arachnoid cysts X-linked lissencephaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arachnoid cysts X-linked spasticity-intellectual disability-epilepsy syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Benign mesial temporal lobe epilepsy Periventricular heterotopia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Corpus callosum agenesis with abnormal genitalia Periventricular heterotopia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Periventricular heterotopia X-linked lissencephaly 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Periventricular heterotopia X-linked spasticity-intellectual disability-epilepsy syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Arachnoid cysts Lissencephaly, x-linked 0.200 1 3.90e-4 8.52e-4 ✓ sig.