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 178

8 diseases · 17 shared-gene connections
8 Diseases
33 Unique genes
0.210 Avg. similarity score
Agammaglobulinemia Most-connected disease (6 links)
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Disease Searched: autosomal agammaglobulinemia 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 6 6 13
Activated pi3k-delta syndrome 5 5 3
Combined immunodeficiency with facio-oculo-skeletal anomalies 5 5 2
immunodeficiency 14 5 5 1
immunodeficiency 14b, autosomal recessive 5 5 1
Roifman syndrome 4 4 3
Burkitt lymphoma 2 2 19
autosomal agammaglobulinemia 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PIK3CD 6 / 8 Activated pi3k-delta syndrome, Agammaglobulinemia, Combined immunodeficiency with facio-oculo-skeletal anomalies, immunodeficiency 14 and 2 more
PIK3R1 3 / 8 Activated pi3k-delta syndrome, Agammaglobulinemia, Burkitt lymphoma
TCF3 3 / 8 Agammaglobulinemia, autosomal agammaglobulinemia, Burkitt lymphoma
KNSTRN 2 / 8 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 ⇵
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
PIK3CD, PIK3R1, CD79A, BLNK, CD79B
 Reactome 5 / 23 79.1× 3.71e-9 3.46e-7 ✓ sig.
Acute myeloid leukemia
PIK3CD, PIK3R1, SPI1, MYC, RUNX1
 KEGG 5 / 68 26.8× 1.05e-6 4.89e-5 ✓ sig.
Central carbon metabolism in cancer
PIK3CD, PIK3R1, PTEN, MYC, RET
 KEGG 5 / 71 25.6× 1.31e-6 5.92e-5 ✓ sig.
Human T-cell leukemia virus 1 infection
PIK3CD, PIK3R1, PTEN, SPI1, TCF3, MYC, HLA-DQA1
 KEGG 7 / 224 11.4× 2.02e-6 8.52e-5 ✓ sig.
B cell receptor signaling pathway
PIK3CD, PIK3R1, CD79A, BLNK, CD79B
 KEGG 5 / 91 20.0× 4.49e-6 1.69e-4 ✓ sig.
Hepatocellular carcinoma
PIK3CD, PIK3R1, PTEN, ARID1A, MYC, SMARCA4
 KEGG 6 / 170 12.8× 5.94e-6 2.11e-4 ✓ sig.
Pathways in cancer
PIK3CD, PIK3R1, PTEN, SPI1, BBC3, GNA13, MYC, RET, RUNX1
 KEGG 9 / 533 6.1× 9.26e-6 3.04e-4 ✓ sig.
Endometrial cancer
PIK3CD, PIK3R1, PTEN, MYC
 KEGG 4 / 59 24.7× 1.93e-5 5.68e-4 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
PIK3CD, PIK3R1, TCF3, ID3, MYC
 KEGG 5 / 144 12.6× 4.19e-5 1.08e-3 ✓ sig.
Chronic myeloid leukemia
PIK3CD, PIK3R1, MYC, RUNX1
 KEGG 4 / 77 18.9× 5.55e-5 1.35e-3 ✓ sig.
CD22 mediated BCR regulation
CD79A, CD79B
 Reactome 2 / 5 146× 7.28e-5 1.68e-3 ✓ sig.
Colorectal cancer
PIK3CD, PIK3R1, BBC3, MYC
 KEGG 4 / 87 16.7× 8.95e-5 2.00e-3 ✓ sig.
Interleukin-7 signaling
PIK3R1, BRWD1, SMARCA4
 Reactome 3 / 33 33.1× 9.75e-5 2.14e-3 ✓ sig.
Small cell lung cancer
PIK3CD, PIK3R1, PTEN, MYC
 KEGG 4 / 93 15.7× 1.16e-4 2.46e-3 ✓ sig.
Primary immunodeficiency
IGLL1, CD79A, BLNK
 KEGG 3 / 38 28.7× 1.49e-4 3.01e-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 ⇵
B cell differentiation
PIK3CD, PIK3R1, SLC39A7, CD79A, BLNK, CD79B, TCF3
 GO:0030183 7 / 80 49.5× 7.87e-11 2.36e-8 ✓ sig.
B cell receptor signaling pathway
PIK3CD, CD79A, BLNK, CD79B
 GO:0050853 4 / 56 40.4× 2.77e-6 1.88e-4 ✓ sig.
negative regulation of wound healing, spreading of epidermal cells
PTEN, CLASP1
 GO:1903690 2 / 5 227× 3.01e-5 1.23e-3 ✓ sig.
positive regulation of DNA-templated transcription
SPI1, TCF3, ARID1A, MLLT11, MYC, RET, SMARCA4, RUNX1
 GO:0045893 8 / 778 5.8× 4.79e-5 1.75e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
SPI1, ARID1A, SMARCA4
 GO:0045815 3 / 41 41.4× 5.11e-5 1.84e-3 ✓ sig.
myeloid leukocyte differentiation
SPI1, RUNX1
 GO:0002573 2 / 7 162× 6.32e-5 2.15e-3 ✓ sig.
B cell activation
PIK3CD, CD79A, BLNK
 GO:0042113 3 / 44 38.6× 6.32e-5 2.15e-3 ✓ sig.
positive regulation of myoblast differentiation
LRRC8A, ARID1A, SMARCA4
 GO:0045663 3 / 47 36.1× 7.72e-5 2.50e-3 ✓ sig.
germinal center B cell differentiation
POU2AF1, SPI1
 GO:0002314 2 / 9 126× 1.08e-4 3.21e-3 ✓ sig.
positive regulation of miRNA transcription
SPI1, MYC, SMARCA4
 GO:1902895 3 / 56 30.3× 1.30e-4 3.71e-3 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
TCF3, ARID1A, SMARCA4
 GO:2000045 3 / 57 29.8× 1.38e-4 3.85e-3 ✓ sig.
fibroblast apoptotic process
BBC3, MYC
 GO:0044346 2 / 11 103× 1.65e-4 4.41e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
PIK3R1, PTEN, POU2AF1, SPI1, TCF3, MYC, PBX1, SMARCA4, RUNX1
 GO:0045944 9 / 1,208 4.2× 1.79e-4 4.67e-3 ✓ sig.
regulation of multicellular organismal development
PIK3CD, RUNX1
 GO:2000026 2 / 15 75.5× 3.13e-4 6.98e-3 ✓ sig.
immune response
PIK3CD, PIK3R1, TNFSF13, IGLL1, CD79B, HLA-DQA1
 GO:0006955 6 / 543 6.3× 3.32e-4 7.26e-3 ✓ 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 1.93e-7 ✓ sig.
Activated pi3k-delta syndrome Agammaglobulinemia 0.133 2 1.97e-6 1.10e-5 ✓ sig.
immunodeficiency 14 immunodeficiency 14b, autosomal recessive 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Combined immunodeficiency with facio-oculo-skeletal anomalies immunodeficiency 14 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Combined immunodeficiency with facio-oculo-skeletal anomalies immunodeficiency 14b, autosomal recessive 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Agammaglobulinemia Burkitt lymphoma 0.065 2 1.12e-4 3.93e-4 ✓ sig.
Activated pi3k-delta syndrome immunodeficiency 14 0.250 1 1.95e-4 5.35e-4 ✓ sig.
immunodeficiency 14b, autosomal recessive Roifman syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
immunodeficiency 14 Roifman syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Activated pi3k-delta syndrome immunodeficiency 14b, autosomal recessive 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Activated pi3k-delta syndrome Combined immunodeficiency with facio-oculo-skeletal anomalies 0.200 1 3.90e-4 8.66e-4 ✓ sig.
Activated pi3k-delta syndrome Roifman syndrome 0.167 1 5.84e-4 1.16e-3 ✓ sig.
Agammaglobulinemia autosomal agammaglobulinemia 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Agammaglobulinemia immunodeficiency 14 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Agammaglobulinemia immunodeficiency 14b, autosomal recessive 0.071 1 8.44e-4 1.50e-3 ✓ sig.
autosomal agammaglobulinemia Burkitt lymphoma 0.050 1 1.23e-3 1.98e-3 ✓ sig.
Agammaglobulinemia Combined immunodeficiency with facio-oculo-skeletal anomalies 0.067 1 1.69e-3 2.53e-3 ✓ sig.