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 358

7 diseases · 10 shared-gene connections
7 Diseases
4 Unique genes
0.325 Avg. similarity score
Bilateral generalized polymicrogyria Most-connected disease (5 links)
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Disease Searched: Microcephaly with or without short stature 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 ⇵
Bilateral generalized polymicrogyria 5 5 2
Microcephalic primordial dwarfism 4 4 2
Microcephaly with or without short stature 3 3 2
Microcephaly, short stature, and polymicrogyria with seizures 3 3 1
Intellectual disability, autosomal dominant 8 2 2 1
Neurodevelopmental disorder with or without hyperkinetic movements and seizures 2 2 1
Microcephaly, epilepsy, cerebral and/or cerebellar atrophy and short stature 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RTTN 4 / 7 Bilateral generalized polymicrogyria, Microcephalic primordial dwarfism, Microcephaly with or without short stature, Microcephaly, short stature, and polymicrogyria with seizures
GRIN1 3 / 7 Bilateral generalized polymicrogyria, Intellectual disability, autosomal dominant 8, Neurodevelopmental disorder with or without hyperkinetic movements and seizures
ZNF335 2 / 7 Microcephalic primordial dwarfism, Microcephaly, epilepsy, cerebral and/or cerebellar atrophy and short stature
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 ⇵
Assembly and cell surface presentation of NMDA receptors
GRIN1
 Reactome 1 / 6 500× 2.00e-3 1.90e-2 ✓ sig.
Synaptic adhesion-like molecules
GRIN1
 Reactome 1 / 21 143× 6.98e-3 4.53e-2 ✓ sig.
Unblocking of NMDA receptors, glutamate binding and activation
GRIN1
 Reactome 1 / 22 136× 7.31e-3 4.67e-2 ✓ sig.
EPHB-mediated forward signaling
GRIN1
 Reactome 1 / 39 77.0× 1.29e-2 6.62e-2
Nicotine addiction
GRIN1
 KEGG 1 / 41 73.2× 1.36e-2 6.85e-2
Cocaine addiction
GRIN1
 KEGG 1 / 49 61.3× 1.62e-2 7.59e-2
Long-term potentiation
GRIN1
 KEGG 1 / 67 44.8× 2.21e-2 9.09e-2
Amphetamine addiction
GRIN1
 KEGG 1 / 69 43.5× 2.28e-2 9.23e-2
Loss of Nlp from mitotic centrosomes
CEP152
 Reactome 1 / 70 42.9× 2.31e-2 9.31e-2
Loss of proteins required for interphase microtubule organization from the centrosome
CEP152
 Reactome 1 / 70 42.9× 2.31e-2 9.31e-2
AURKA Activation by TPX2
CEP152
 Reactome 1 / 73 41.1× 2.41e-2 9.55e-2
Recruitment of mitotic centrosome proteins and complexes
CEP152
 Reactome 1 / 82 36.6× 2.70e-2 1.02e-1
Regulation of PLK1 Activity at G2/M Transition
CEP152
 Reactome 1 / 88 34.1× 2.90e-2 1.06e-1
Recruitment of NuMA to mitotic centrosomes
CEP152
 Reactome 1 / 94 31.9× 3.09e-2 1.10e-1
Circadian entrainment
GRIN1
 KEGG 1 / 97 31.0× 3.19e-2 1.12e-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 ⇵
centriole replication
RTTN, CEP152
 GO:0007099 2 / 24 389× 9.47e-6 5.21e-4 ✓ sig.
propylene metabolic process
GRIN1
 GO:0018964 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
response to glycine
GRIN1
 GO:1905429 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
brain development
GRIN1, ZNF335
 GO:0007420 2 / 244 38.3× 1.00e-3 1.46e-2 ✓ sig.
ciliary basal body organization
RTTN
 GO:0032053 1 / 5 934× 1.07e-3 1.51e-2 ✓ sig.
de novo centriole assembly involved in multi-ciliated epithelial cell differentiation
CEP152
 GO:0098535 1 / 5 934× 1.07e-3 1.51e-2 ✓ sig.
positive regulation of lymphocyte proliferation
ZNF335
 GO:0050671 1 / 9 519× 1.93e-3 2.07e-2 ✓ sig.
calcium ion transmembrane import into cytosol
GRIN1
 GO:0097553 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
regulation of monoatomic cation transmembrane transport
GRIN1
 GO:1904062 1 / 10 467× 2.14e-3 2.19e-2 ✓ sig.
centriole-centriole cohesion
RTTN
 GO:0010457 1 / 13 359× 2.78e-3 2.51e-2 ✓ sig.
excitatory chemical synaptic transmission
GRIN1
 GO:0098976 1 / 13 359× 2.78e-3 2.51e-2 ✓ sig.
positive regulation of calcium ion transport into cytosol
GRIN1
 GO:0010524 1 / 14 334× 2.99e-3 2.59e-2 ✓ sig.
protein heterotetramerization
GRIN1
 GO:0051290 1 / 16 292× 3.42e-3 2.78e-2 ✓ sig.
cerebral cortex neuron differentiation
ZNF335
 GO:0021895 1 / 16 292× 3.42e-3 2.78e-2 ✓ sig.
positive regulation of reactive oxygen species biosynthetic process
GRIN1
 GO:1903428 1 / 17 275× 3.63e-3 2.86e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Intellectual disability, autosomal dominant 8 Neurodevelopmental disorder with or without hyperkinetic movements and seizures 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Bilateral generalized polymicrogyria Neurodevelopmental disorder with or without hyperkinetic movements and seizures 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bilateral generalized polymicrogyria Intellectual disability, autosomal dominant 8 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bilateral generalized polymicrogyria Microcephaly, short stature, and polymicrogyria with seizures 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Microcephalic primordial dwarfism Microcephaly, epilepsy, cerebral and/or cerebellar atrophy and short stature 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Microcephalic primordial dwarfism Microcephaly, short stature, and polymicrogyria with seizures 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Microcephaly with or without short stature Microcephaly, short stature, and polymicrogyria with seizures 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bilateral generalized polymicrogyria Microcephalic primordial dwarfism 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Bilateral generalized polymicrogyria Microcephaly with or without short stature 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Microcephalic primordial dwarfism Microcephaly with or without short stature 0.250 1 2.58e-4 5.38e-4 ✓ sig.