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 220

8 diseases · 13 shared-gene connections
8 Diseases
9 Unique genes
0.220 Avg. similarity score
Cortical dysplasia 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 ⇵
Cortical dysplasia 5 5 4
Developmental delay with language impairment and movement disorder 5 5 2
Intellectual developmental disorder autism speech 5 5 2
Cortical occipital malformations 4 4 2
Intellectual developmental disorder speech autism dysmorphic 4 4 3
Intellectual developmental disorder language neurodegenerative 1 1 1
intellectual developmental disorder with autistic features and language delay, with or without seizures 1 1 1
lethal osteosclerotic bone dysplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBR1 5 / 8 Cortical dysplasia, Cortical occipital malformations, Developmental delay with language impairment and movement disorder, Intellectual developmental disorder autism speech and 1 more
FAM20C 2 / 8 Cortical dysplasia, lethal osteosclerotic bone dysplasia
NR4A2 2 / 8 Developmental delay with language impairment and movement disorder, Intellectual developmental disorder language neurodegenerative
TANC2 2 / 8 Intellectual developmental disorder autism speech, intellectual developmental disorder with autistic features and language delay, with or without seizures
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 ⇵
Inhibition of TSC complex formation by PKB
TSC1
 Reactome 1 / 3 445× 2.25e-3 2.48e-2 ✓ sig.
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
CNOT3
 Reactome 1 / 20 66.7× 1.49e-2 8.66e-2
Deadenylation of mRNA
CNOT3
 Reactome 1 / 24 55.6× 1.78e-2 9.67e-2
Laminin interactions
LAMC3
 Reactome 1 / 28 47.7× 2.08e-2 1.05e-1
Energy dependent regulation of mTOR by LKB1-AMPK
TSC1
 Reactome 1 / 29 46.0× 2.15e-2 1.07e-1
MET activates PTK2 signaling
LAMC3
 Reactome 1 / 30 44.5× 2.23e-2 1.09e-1
Human papillomavirus infection
TSC1, LAMC3
 KEGG 2 / 333 8.0× 2.43e-2 1.15e-1
PI3K-Akt signaling pathway
TSC1, LAMC3
 KEGG 2 / 361 7.4× 2.82e-2 1.25e-1
TBC/RABGAPs
TSC1
 Reactome 1 / 46 29.0× 3.40e-2 1.38e-1
Nuclear Receptor transcription pathway
NR4A2
 Reactome 1 / 52 25.7× 3.83e-2 1.48e-1
Macroautophagy
TSC1
 Reactome 1 / 68 19.6× 4.98e-2 1.71e-1
Non-small cell lung cancer
KIF5C
 KEGG 1 / 73 18.3× 5.34e-2 1.78e-1
RNA degradation
CNOT3
 KEGG 1 / 78 17.1× 5.70e-2 1.84e-1
TP53 Regulates Metabolic Genes
TSC1
 Reactome 1 / 86 15.5× 6.27e-2 1.93e-1
ECM-receptor interaction
LAMC3
 KEGG 1 / 89 15.0× 6.48e-2 1.96e-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 ⇵
adult locomotory behavior
TSC1, NR4A2
 GO:0008344 2 / 56 74.2× 3.13e-4 6.93e-3 ✓ sig.
general adaptation syndrome
NR4A2
 GO:0051866 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
specification of animal organ identity
TBR1
 GO:0010092 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
memory T cell differentiation
TSC1
 GO:0043379 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
cerebral cortex development
TBR1, TSC1
 GO:0021987 2 / 88 47.2× 7.73e-4 1.28e-2 ✓ sig.
osteoclast maturation
FAM20C
 GO:0036179 1 / 2 1,038× 9.63e-4 1.47e-2 ✓ sig.
regulation of phosphorus metabolic process
FAM20C
 GO:0051174 1 / 2 1,038× 9.63e-4 1.47e-2 ✓ sig.
anterograde dendritic transport of messenger ribonucleoprotein complex
KIF5C
 GO:0098964 1 / 3 692× 1.44e-3 1.87e-2 ✓ sig.
conditioned taste aversion
TBR1
 GO:0001661 1 / 3 692× 1.44e-3 1.87e-2 ✓ sig.
habenula development
NR4A2
 GO:0021986 1 / 3 692× 1.44e-3 1.87e-2 ✓ sig.
amygdala development
TBR1
 GO:0021764 1 / 4 519× 1.93e-3 2.20e-2 ✓ sig.
dense core granule cytoskeletal transport
TANC2
 GO:0099519 1 / 4 519× 1.93e-3 2.20e-2 ✓ sig.
cellular response to decreased oxygen levels
TSC1
 GO:0036294 1 / 4 519× 1.93e-3 2.20e-2 ✓ sig.
cellular response to corticotropin-releasing hormone stimulus
NR4A2
 GO:0071376 1 / 5 415× 2.41e-3 2.50e-2 ✓ sig.
organelle organization
KIF5C
 GO:0006996 1 / 5 415× 2.41e-3 2.50e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Developmental delay with language impairment and movement disorder Intellectual developmental disorder language neurodegenerative 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Intellectual developmental disorder autism speech intellectual developmental disorder with autistic features and language delay, with or without seizures 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cortical occipital malformations Developmental delay with language impairment and movement disorder 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Cortical occipital malformations Intellectual developmental disorder autism speech 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Developmental delay with language impairment and movement disorder Intellectual developmental disorder autism speech 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Cortical dysplasia lethal osteosclerotic bone dysplasia 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cortical occipital malformations Intellectual developmental disorder speech autism dysmorphic 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Developmental delay with language impairment and movement disorder Intellectual developmental disorder speech autism dysmorphic 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Intellectual developmental disorder autism speech Intellectual developmental disorder speech autism dysmorphic 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Cortical dysplasia Cortical occipital malformations 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cortical dysplasia Developmental delay with language impairment and movement disorder 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cortical dysplasia Intellectual developmental disorder autism speech 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cortical dysplasia Intellectual developmental disorder speech autism dysmorphic 0.143 1 7.79e-4 1.39e-3 ✓ sig.