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 323

6 diseases · 8 shared-gene connections
6 Diseases
23 Unique genes
0.142 Avg. similarity score
Silver-russell 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 ⇵
Silver-russell syndrome 5 5 11
Beckwith-wiedemann syndrome 3 3 10
Russell-silver syndrome 3 3 7
Childhood apraxia of speech 2 2 1
Chorioretinal atrophy 2 2 2
Chromosomal disorder 1 1 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
- 3 / 6 Beckwith-wiedemann syndrome, Chorioretinal atrophy, Silver-russell syndrome
CDKN1C 3 / 6 Beckwith-wiedemann syndrome, Russell-silver syndrome, Silver-russell syndrome
FOXP2 3 / 6 Childhood apraxia of speech, Russell-silver syndrome, Silver-russell syndrome
IGF2 3 / 6 Beckwith-wiedemann syndrome, Russell-silver syndrome, Silver-russell syndrome
GRB10 2 / 6 Chromosomal disorder, Silver-russell syndrome
HMGA2 2 / 6 Russell-silver syndrome, Silver-russell syndrome
INS-IGF2 2 / 6 Beckwith-wiedemann syndrome, Silver-russell syndrome
PLAG1 2 / 6 Russell-silver syndrome, Silver-russell 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 ⇵
Prolactin receptor signaling
CSH1, GH2
 Reactome 2 / 12 87.0× 2.29e-4 4.35e-3 ✓ sig.
Growth hormone receptor signaling
CSH1, GH2
 Reactome 2 / 14 74.6× 3.15e-4 5.57e-3 ✓ sig.
Hormone signaling
IGF2, PIK3CA, CSH1, GH2
 KEGG 4 / 219 9.5× 7.25e-4 1.07e-2 ✓ sig.
Growth hormone synthesis, secretion and action
PIK3CA, CSH1, GH2
 KEGG 3 / 122 12.8× 1.56e-3 1.90e-2 ✓ sig.
Signaling by SCF-KIT
PIK3CA, GRB10
 Reactome 2 / 37 28.2× 2.24e-3 2.48e-2 ✓ sig.
RET signaling
PIK3CA, GRB10
 Reactome 2 / 40 26.1× 2.62e-3 2.79e-2 ✓ sig.
JAK-STAT signaling pathway
PIK3CA, CSH1, GH2
 KEGG 3 / 168 9.3× 3.88e-3 3.69e-2 ✓ sig.
PI3K-Akt signaling pathway
IGF2, PIK3CA, CSH1, GH2
 KEGG 4 / 361 5.8× 4.52e-3 4.10e-2 ✓ sig.
SUMOylation of DNA methylation proteins
DNMT1
 Reactome 1 / 4 131× 7.64e-3 5.79e-2
Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
IGF2
 Reactome 1 / 4 131× 7.64e-3 5.79e-2
IRS activation
GRB10
 Reactome 1 / 5 104× 9.54e-3 6.67e-2
MET activates PI3K/AKT signaling
PIK3CA
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
SHC-related events triggered by IGF1R
IGF2
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
Insulin receptor signalling cascade
GRB10
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-2
IRS-related events triggered by IGF1R
IGF2
 Reactome 1 / 6 87.0× 1.14e-2 7.44e-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 ⇵
insulin-like growth factor receptor signaling pathway
IGF2, IGF2R, PIK3CA, GRB10
 GO:0048009 4 / 33 98.5× 6.97e-8 8.94e-6 ✓ sig.
embryonic placenta morphogenesis
CDKN1C, IGF2
 GO:0060669 2 / 5 325× 1.45e-5 6.96e-4 ✓ sig.
negative regulation of transcription by RNA polymerase II
CDKN1C, DNMT1, IGF2, NSD1, FOXP2, FLYWCH1, HMGA2, ARX
 GO:0000122 8 / 1,002 6.5× 1.58e-5 7.50e-4 ✓ sig.
positive regulation of epithelial cell proliferation involved in lung morphogenesis
FOXP2, HMGA2
 GO:0060501 2 / 7 232× 3.03e-5 1.23e-3 ✓ sig.
cardiac muscle cell contraction
KCNQ1, PIK3CA
 GO:0086003 2 / 10 162× 6.48e-5 2.18e-3 ✓ sig.
glucose metabolic process
IGF2, KCNQ1, PIK3CA
 GO:0006006 3 / 66 36.9× 7.08e-5 2.34e-3 ✓ sig.
positive regulation of organ growth
IGF2, ARX
 GO:0046622 2 / 13 125× 1.12e-4 3.29e-3 ✓ sig.
insulin receptor signaling pathway
IGF2, PIK3CA, GRB10
 GO:0008286 3 / 80 30.5× 1.26e-4 3.59e-3 ✓ sig.
cell proliferation in forebrain
HMGA2, ARX
 GO:0021846 2 / 14 116× 1.31e-4 3.70e-3 ✓ sig.
liver development
IGF2R, PIK3CA, COBL
 GO:0001889 3 / 87 28.0× 1.61e-4 4.33e-3 ✓ sig.
growth hormone receptor signaling pathway
CSH1, GH2
 GO:0060396 2 / 16 102× 1.72e-4 4.54e-3 ✓ sig.
genomic imprinting
CDKN1C, IGF2
 GO:0071514 2 / 17 95.6× 1.95e-4 4.96e-3 ✓ sig.
animal organ development
FOXP2, CSH1, GH2
 GO:0048513 3 / 102 23.9× 2.58e-4 6.05e-3 ✓ sig.
multicellular organism growth
CDKN1C, HMGA2, PLAG1
 GO:0035264 3 / 115 21.2× 3.68e-4 7.71e-3 ✓ sig.
adrenal gland development
CDKN1C, HMGA2
 GO:0030325 2 / 24 67.7× 3.93e-4 8.11e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Russell-silver syndrome Silver-russell syndrome 0.357 5 1.34e-15 2.11e-14 ✓ sig.
Beckwith-wiedemann syndrome Silver-russell syndrome 0.222 4 2.95e-11 3.28e-10 ✓ sig.
Beckwith-wiedemann syndrome Russell-silver syndrome 0.125 2 7.96e-6 4.23e-5 ✓ sig.
Childhood apraxia of speech Russell-silver syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Childhood apraxia of speech Silver-russell syndrome 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Beckwith-wiedemann syndrome Chorioretinal atrophy 0.083 1 1.30e-3 2.04e-3 ✓ sig.
Chorioretinal atrophy Silver-russell syndrome 0.077 1 1.43e-3 2.21e-3 ✓ sig.
Chromosomal disorder Silver-russell syndrome 0.067 1 2.85e-3 3.80e-3 ✓ sig.