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 375

5 diseases · 10 shared-gene connections
5 Diseases
5 Unique genes
0.303 Avg. similarity score
Activated pi3k-delta syndrome Most-connected disease (4 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 ⇵
Activated pi3k-delta syndrome 4 4 3
Combined immunodeficiency with facio-oculo-skeletal anomalies 4 4 2
Roifman syndrome 4 4 3
immunodeficiency 14 4 4 1
immunodeficiency 14b, autosomal recessive 4 4 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PIK3CD 5 / 5 Activated pi3k-delta syndrome, Combined immunodeficiency with facio-oculo-skeletal anomalies, immunodeficiency 14, immunodeficiency 14b, autosomal recessive and 1 more
KNSTRN 2 / 5 Combined immunodeficiency with facio-oculo-skeletal anomalies, Roifman 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 ⇵
Synthesis of PIPs at the plasma membrane
PIK3CD, PIK3R1, PTEN
 Reactome 3 / 51 141× 7.17e-7 3.65e-5 ✓ sig.
Endometrial cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 59 122× 1.12e-6 5.39e-5 ✓ sig.
Central carbon metabolism in cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 71 101× 1.96e-6 8.64e-5 ✓ sig.
Melanoma
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 73 98.7× 2.14e-6 9.29e-5 ✓ sig.
Glioma
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 76 94.8× 2.41e-6 1.04e-4 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 80 90.1× 2.82e-6 1.18e-4 ✓ sig.
PD-L1 expression and PD-1 checkpoint pathway in cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 90 80.1× 4.03e-6 1.59e-4 ✓ sig.
Small cell lung cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 93 77.5× 4.45e-6 1.73e-4 ✓ sig.
Phosphatidylinositol signaling system
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 98 73.5× 5.21e-6 1.96e-4 ✓ sig.
Prostate cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 98 73.5× 5.21e-6 1.96e-4 ✓ sig.
Insulin resistance
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 109 66.1× 7.18e-6 2.54e-4 ✓ sig.
Erythropoietin activates Phosphoinositide-3-kinase (PI3K)
PIK3CD, PIK3R1
 Reactome 2 / 12 400× 9.14e-6 3.12e-4 ✓ sig.
Sphingolipid signaling pathway
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 122 59.1× 1.01e-5 3.38e-4 ✓ sig.
FoxO signaling pathway
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 133 54.2× 1.31e-5 4.19e-4 ✓ sig.
Breast cancer
PIK3CD, PIK3R1, PTEN
 KEGG 3 / 148 48.7× 1.80e-5 5.49e-4 ✓ 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 ⇵
negative regulation of wound healing, spreading of epidermal cells
PTEN, CLASP1
 GO:1903690 2 / 5 1,495× 5.73e-7 5.25e-5 ✓ sig.
phosphatidylinositol 3-kinase/protein kinase B signal transduction
PIK3CD, PIK3R1, PTEN
 GO:0043491 3 / 92 122× 1.15e-6 9.25e-5 ✓ sig.
negative regulation of stress fiber assembly
PIK3R1, CLASP1
 GO:0051497 2 / 33 227× 3.01e-5 1.22e-3 ✓ sig.
cell migration
PIK3CD, PTEN, KNSTRN
 GO:0016477 3 / 303 37.0× 4.12e-5 1.56e-3 ✓ sig.
phosphatidylinositol phosphate biosynthetic process
PIK3CD, PIK3R1
 GO:0046854 2 / 43 174× 5.15e-5 1.84e-3 ✓ sig.
T cell differentiation
PIK3CD, PIK3R1
 GO:0030217 2 / 54 138× 8.15e-5 2.59e-3 ✓ sig.
B cell differentiation
PIK3CD, PIK3R1
 GO:0030183 2 / 80 93.4× 1.79e-4 4.68e-3 ✓ sig.
negative regulation of cell communication
PTEN
 GO:0010648 1 / 1 3,737× 2.68e-4 6.20e-3 ✓ sig.
negative regulation of synaptic vesicle clustering
PTEN
 GO:2000808 1 / 1 3,737× 2.68e-4 6.20e-3 ✓ sig.
positive regulation of endoplasmic reticulum unfolded protein response
PIK3R1
 GO:1900103 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
natural killer cell chemotaxis
PIK3CD
 GO:0035747 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
negative regulation of keratinocyte migration
PTEN
 GO:0051548 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
positive regulation of basement membrane assembly involved in embryonic body morphogenesis
CLASP1
 GO:1904261 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
negative regulation of microtubule polymerization or depolymerization
CLASP1
 GO:0031111 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
microtubule cytoskeleton organization
KNSTRN, CLASP1
 GO:0000226 2 / 149 50.2× 6.22e-4 1.11e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Combined immunodeficiency with facio-oculo-skeletal anomalies Roifman syndrome 0.500 2 2.53e-8 2.03e-7 ✓ sig.
immunodeficiency 14 immunodeficiency 14b, autosomal recessive 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Combined immunodeficiency with facio-oculo-skeletal anomalies immunodeficiency 14b, autosomal recessive 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined immunodeficiency with facio-oculo-skeletal anomalies immunodeficiency 14 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Activated pi3k-delta syndrome immunodeficiency 14b, autosomal recessive 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Activated pi3k-delta syndrome immunodeficiency 14 0.250 1 1.95e-4 5.28e-4 ✓ sig.
immunodeficiency 14 Roifman syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
immunodeficiency 14b, autosomal recessive Roifman syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Activated pi3k-delta syndrome Combined immunodeficiency with facio-oculo-skeletal anomalies 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Activated pi3k-delta syndrome Roifman syndrome 0.167 1 5.84e-4 1.14e-3 ✓ sig.