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 260

8 diseases · 19 shared-gene connections
8 Diseases
15 Unique genes
0.320 Avg. similarity score
Agammaglobulinemia 7, autosomal recessive Most-connected disease (6 links)
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Disease Searched: Immunodeficiency and SHORT syndrome 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 ⇵
Agammaglobulinemia 7, autosomal recessive 6 6 1
Immunodeficiency 36 with lymphoproliferation 6 6 1
Immunodeficiency and SHORT syndrome 6 6 1
Short syndrome 6 6 1
Diffuse idiopathic skeletal hyperostosis 5 5 11
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 4 4 3
Malignant breast myoepithelioma 4 4 3
Immunodeficiency 122 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PIK3R1 7 / 8 Agammaglobulinemia 7, autosomal recessive, Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi, Diffuse idiopathic skeletal hyperostosis, Immunodeficiency 36 with lymphoproliferation and 3 more
POLD3 2 / 8 Diffuse idiopathic skeletal hyperostosis, Immunodeficiency 122
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 ⇵
Thyroid hormone signaling pathway
PIK3CA, PIK3R1, MED30, TP53
 KEGG 4 / 122 26.3× 1.27e-5 3.55e-4 ✓ sig.
MET activates PI3K/AKT signaling
PIK3CA, PIK3R1
 Reactome 2 / 6 267× 2.18e-5 5.59e-4 ✓ sig.
IRS-mediated signalling
PIK3CA, PIK3R1
 Reactome 2 / 6 267× 2.18e-5 5.59e-4 ✓ sig.
Endometrial cancer
PIK3CA, PIK3R1, TP53
 KEGG 3 / 59 40.7× 4.91e-5 1.08e-3 ✓ sig.
Activation of PUMA and translocation to mitochondria
TP63, TP53
 Reactome 2 / 9 178× 5.22e-5 1.13e-3 ✓ sig.
PI3K/AKT activation
PIK3CA, PIK3R1
 Reactome 2 / 9 178× 5.22e-5 1.13e-3 ✓ sig.
PI3K events in ERBB4 signaling
PIK3CA, PIK3R1
 Reactome 2 / 10 160× 6.51e-5 1.34e-3 ✓ sig.
Signaling by FGFR3 fusions in cancer
PIK3CA, PIK3R1
 Reactome 2 / 10 160× 6.51e-5 1.34e-3 ✓ sig.
GnRH secretion
GNA11, PIK3CA, PIK3R1
 KEGG 3 / 65 37.0× 6.57e-5 1.36e-3 ✓ sig.
Signaling by FGFR4 in disease
PIK3CA, PIK3R1
 Reactome 2 / 11 146× 7.96e-5 1.58e-3 ✓ sig.
Costimulation by the CD28 family
PIK3CA, PIK3R1
 Reactome 2 / 11 146× 7.96e-5 1.58e-3 ✓ sig.
Central carbon metabolism in cancer
PIK3CA, PIK3R1, TP53
 KEGG 3 / 71 33.8× 8.56e-5 1.68e-3 ✓ sig.
Melanoma
PIK3CA, PIK3R1, TP53
 KEGG 3 / 73 32.9× 9.30e-5 1.80e-3 ✓ sig.
Non-small cell lung cancer
PIK3CA, PIK3R1, TP53
 KEGG 3 / 73 32.9× 9.30e-5 1.80e-3 ✓ sig.
TP53 Regulates Transcription of Death Receptors and Ligands
TP63, TP53
 Reactome 2 / 12 133× 9.54e-5 1.83e-3 ✓ sig.

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
transcription by RNA polymerase II
PIK3R1, NFIL3, SUPT3H, TP63
 GO:0006366 4 / 261 19.1× 4.50e-5 1.71e-3 ✓ sig.
cranial skeletal system development
GNA11, TP63
 GO:1904888 2 / 18 138× 9.13e-5 2.89e-3 ✓ sig.
positive regulation of lamellipodium assembly
PIK3CA, PIK3R1
 GO:0010592 2 / 28 89.0× 2.25e-4 5.51e-3 ✓ sig.
protein tetramerization
TP63, TP53
 GO:0051262 2 / 29 85.9× 2.41e-4 5.79e-3 ✓ sig.
positive regulation of DNA-templated transcription
MED30, NFIL3, SUPT3H, TP63, TP53
 GO:0045893 5 / 778 8.0× 2.62e-4 6.16e-3 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
TP63, TP53
 GO:0042771 2 / 33 75.5× 3.13e-4 6.99e-3 ✓ sig.
insulin-like growth factor receptor signaling pathway
PIK3CA, PIK3R1
 GO:0048009 2 / 33 75.5× 3.13e-4 6.99e-3 ✓ sig.
determination of adult lifespan
TP63, TP53
 GO:0008340 2 / 38 65.6× 4.16e-4 8.41e-3 ✓ sig.
phosphatidylinositol phosphate biosynthetic process
PIK3CA, PIK3R1
 GO:0046854 2 / 43 57.9× 5.33e-4 9.88e-3 ✓ sig.
positive regulation of smooth muscle cell proliferation
PIK3CA, PIK3R1
 GO:0048661 2 / 52 47.9× 7.79e-4 1.26e-2 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.
ectoderm and mesoderm interaction
TP63
 GO:0007499 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.
epidermal cell division
TP63
 GO:0010481 1 / 1 1,246× 8.03e-4 1.28e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Agammaglobulinemia 7, autosomal recessive Immunodeficiency and SHORT syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Agammaglobulinemia 7, autosomal recessive Immunodeficiency 36 with lymphoproliferation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Agammaglobulinemia 7, autosomal recessive Short syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Immunodeficiency and SHORT syndrome Short syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Immunodeficiency 36 with lymphoproliferation Immunodeficiency and SHORT syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Immunodeficiency 36 with lymphoproliferation Short syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant breast myoepithelioma Short syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Immunodeficiency and SHORT syndrome Malignant breast myoepithelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Immunodeficiency 36 with lymphoproliferation Malignant breast myoepithelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi Immunodeficiency 36 with lymphoproliferation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi Immunodeficiency and SHORT syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi Short syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Agammaglobulinemia 7, autosomal recessive Malignant breast myoepithelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Agammaglobulinemia 7, autosomal recessive Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Diffuse idiopathic skeletal hyperostosis Immunodeficiency and SHORT syndrome 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Agammaglobulinemia 7, autosomal recessive Diffuse idiopathic skeletal hyperostosis 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Diffuse idiopathic skeletal hyperostosis Immunodeficiency 36 with lymphoproliferation 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Diffuse idiopathic skeletal hyperostosis Immunodeficiency 122 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Diffuse idiopathic skeletal hyperostosis Short syndrome 0.083 1 7.10e-4 1.17e-3 ✓ sig.