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 455

6 diseases · 8 shared-gene connections
6 Diseases
21 Unique genes
0.217 Avg. similarity score
Dandy-walker syndrome 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 ⇵
Dandy-walker syndrome 5 5 21
Joubert syndrome 21 3 3 1
Joubert syndrome with jeune asphyxiating thoracic dystrophy 3 3 1
Joubert syndrome with or without jeune asphyxiating thoracic dystrophy 3 3 1
Congenital cerebral hernia 1 1 1
Joubert syndrome 30 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CSPP1 4 / 6 Dandy-walker syndrome, Joubert syndrome 21, Joubert syndrome with jeune asphyxiating thoracic dystrophy, Joubert syndrome with or without jeune asphyxiating thoracic dystrophy
ARMC9 2 / 6 Dandy-walker syndrome, Joubert syndrome 30
PIBF1 2 / 6 Congenital cerebral hernia, Dandy-walker syndrome
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 ⇵
Focal adhesion
BRAF, PDGFRB, PPP1CB
 KEGG 3 / 203 8.5× 5.06e-3 3.67e-2 ✓ sig.
Lysine degradation
KMT2D, SETD2
 KEGG 2 / 63 18.2× 5.33e-3 3.81e-2 ✓ sig.
Long-term potentiation
BRAF, PPP1CB
 KEGG 2 / 67 17.1× 6.01e-3 4.11e-2 ✓ sig.
PKMTs methylate histone lysines
KMT2D, SETD2
 Reactome 2 / 71 16.1× 6.73e-3 4.43e-2 ✓ sig.
Melanoma
BRAF, PDGFRB
 KEGG 2 / 73 15.7× 7.10e-3 4.59e-2 ✓ sig.
Regulation of actin cytoskeleton
BRAF, PDGFRB, PPP1CB
 KEGG 3 / 232 7.4× 7.32e-3 4.67e-2 ✓ sig.
Glioma
BRAF, PDGFRB
 KEGG 2 / 76 15.1× 7.68e-3 4.82e-2 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
BRAF, PDGFRB
 KEGG 2 / 80 14.3× 8.48e-3 5.13e-2
Regulation of PLK1 Activity at G2/M Transition
PPP1CB, TUBA1A
 Reactome 2 / 88 13.0× 1.02e-2 5.75e-2
Gap junction
PDGFRB, TUBA1A
 KEGG 2 / 89 12.9× 1.04e-2 5.84e-2
Negative feedback regulation of MAPK pathway
BRAF
 Reactome 1 / 6 95.3× 1.04e-2 5.84e-2
Synthesis of diphthamide-EEF2
DPH1
 Reactome 1 / 7 81.7× 1.22e-2 6.41e-2
Prostate cancer
BRAF, PDGFRB
 KEGG 2 / 98 11.7× 1.25e-2 6.52e-2
Frs2-mediated activation
BRAF
 Reactome 1 / 12 47.7× 2.08e-2 8.77e-2
Vascular smooth muscle contraction
BRAF, PPP1CB
 KEGG 2 / 134 8.5× 2.26e-2 9.18e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
cell migration involved in coronary angiogenesis
PDGFRB
 GO:0060981 1 / 1 890× 1.12e-3 1.55e-2 ✓ sig.
metanephric glomerular mesangial cell proliferation involved in metanephros development
PDGFRB
 GO:0072262 1 / 1 890× 1.12e-3 1.55e-2 ✓ sig.
glomerular epithelium development
FOXC1
 GO:0072010 1 / 1 890× 1.12e-3 1.55e-2 ✓ sig.
positive regulation of hematopoietic stem cell differentiation
FOXC1
 GO:1902038 1 / 1 890× 1.12e-3 1.55e-2 ✓ sig.
beta-catenin-TCF complex assembly
KMT2D
 GO:1904837 1 / 1 890× 1.12e-3 1.55e-2 ✓ sig.
visual learning
BRAF, TUBA1A
 GO:0008542 2 / 54 33.0× 1.66e-3 1.93e-2 ✓ sig.
pattern specification process
MID1, ZIC1
 GO:0007389 2 / 60 29.7× 2.05e-3 2.15e-2 ✓ sig.
cell migration involved in vasculogenesis
PDGFRB
 GO:0035441 1 / 2 445× 2.25e-3 2.24e-2 ✓ sig.
smooth muscle cell chemotaxis
PDGFRB
 GO:0071670 1 / 2 445× 2.25e-3 2.24e-2 ✓ sig.
apoptotic process involved in outflow tract morphogenesis
FOXC1
 GO:0003275 1 / 2 445× 2.25e-3 2.24e-2 ✓ sig.
negative regulation of apoptotic process involved in outflow tract morphogenesis
FOXC1
 GO:1902257 1 / 2 445× 2.25e-3 2.24e-2 ✓ sig.
maintenance of cell number
ZIC1
 GO:0098727 1 / 2 445× 2.25e-3 2.24e-2 ✓ sig.
cilium assembly
PIBF1, ARMC9, HYLS1
 GO:0060271 3 / 237 11.3× 2.26e-3 2.26e-2 ✓ sig.
hippocampus development
TUBA1A, ZIC1
 GO:0021766 2 / 74 24.1× 3.09e-3 2.65e-2 ✓ sig.
positive T cell selection
BRAF
 GO:0043368 1 / 3 297× 3.37e-3 2.76e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Joubert syndrome 21 Joubert syndrome with or without jeune asphyxiating thoracic dystrophy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Joubert syndrome 21 Joubert syndrome with jeune asphyxiating thoracic dystrophy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Joubert syndrome with jeune asphyxiating thoracic dystrophy Joubert syndrome with or without jeune asphyxiating thoracic dystrophy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital cerebral hernia Dandy-walker syndrome 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Dandy-walker syndrome Joubert syndrome 21 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Dandy-walker syndrome Joubert syndrome 30 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Dandy-walker syndrome Joubert syndrome with jeune asphyxiating thoracic dystrophy 0.048 1 1.29e-3 1.89e-3 ✓ sig.
Dandy-walker syndrome Joubert syndrome with or without jeune asphyxiating thoracic dystrophy 0.048 1 1.29e-3 1.89e-3 ✓ sig.