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 184

8 diseases · 8 shared-gene connections
8 Diseases
30 Unique genes
0.068 Avg. similarity score
Agammaglobulinemia Most-connected disease (7 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 ⇵
Agammaglobulinemia 7 7 13
Burkitt lymphoma 2 2 19
autosomal agammaglobulinemia 2 2 1
agammaglobulinemia 10, autosomal dominant 1 1 1
agammaglobulinemia 2, autosomal recessive 1 1 1
agammaglobulinemia 3, autosomal recessive 1 1 1
agammaglobulinemia 4, autosomal recessive 1 1 1
agammaglobulinemia 6, autosomal recessive 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TCF3 3 / 8 Agammaglobulinemia, autosomal agammaglobulinemia, Burkitt lymphoma
BLNK 2 / 8 Agammaglobulinemia, agammaglobulinemia 4, autosomal recessive
CD79A 2 / 8 Agammaglobulinemia, agammaglobulinemia 3, autosomal recessive
CD79B 2 / 8 Agammaglobulinemia, agammaglobulinemia 6, autosomal recessive
IGLL1 2 / 8 Agammaglobulinemia, agammaglobulinemia 2, autosomal recessive
PIK3R1 2 / 8 Agammaglobulinemia, Burkitt lymphoma
SPI1 2 / 8 Agammaglobulinemia, agammaglobulinemia 10, autosomal dominant
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
CD79A, BLNK, CD79B, PIK3R1, PIK3CD
 Reactome 5 / 23 87.0× 2.23e-9 2.27e-7 ✓ sig.
Acute myeloid leukemia
SPI1, PIK3R1, PIK3CD, MYC, RUNX1
 KEGG 5 / 68 29.4× 6.40e-7 3.31e-5 ✓ sig.
B cell receptor signaling pathway
CD79A, BLNK, CD79B, PIK3R1, PIK3CD
 KEGG 5 / 91 22.0× 2.74e-6 1.15e-4 ✓ sig.
Human T-cell leukemia virus 1 infection
SPI1, PIK3R1, TCF3, PIK3CD, MYC, HLA-DQA1
 KEGG 6 / 224 10.7× 1.61e-5 4.98e-4 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
PIK3R1, TCF3, PIK3CD, ID3, MYC
 KEGG 5 / 144 13.9× 2.59e-5 7.36e-4 ✓ sig.
Central carbon metabolism in cancer
PIK3R1, PIK3CD, MYC, RET
 KEGG 4 / 71 22.6× 2.74e-5 7.71e-4 ✓ sig.
Pathways in cancer
SPI1, PIK3R1, PIK3CD, BBC3, GNA13, MYC, RET, RUNX1
 KEGG 8 / 533 6.0× 3.51e-5 9.54e-4 ✓ sig.
Chronic myeloid leukemia
PIK3R1, PIK3CD, MYC, RUNX1
 KEGG 4 / 77 20.8× 3.77e-5 1.01e-3 ✓ sig.
Hepatocellular carcinoma
PIK3R1, PIK3CD, ARID1A, MYC, SMARCA4
 KEGG 5 / 170 11.8× 5.73e-5 1.43e-3 ✓ sig.
CD22 mediated BCR regulation
CD79A, CD79B
 Reactome 2 / 5 160× 6.00e-5 1.48e-3 ✓ sig.
Colorectal cancer
PIK3R1, PIK3CD, BBC3, MYC
 KEGG 4 / 87 18.4× 6.10e-5 1.50e-3 ✓ sig.
Interleukin-7 signaling
BRWD1, PIK3R1, SMARCA4
 Reactome 3 / 33 36.4× 7.30e-5 1.73e-3 ✓ sig.
Primary immunodeficiency
IGLL1, CD79A, BLNK
 KEGG 3 / 38 31.6× 1.12e-4 2.46e-3 ✓ sig.
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
ARID1A, SMARCA4, RUNX1
 Reactome 3 / 38 31.6× 1.12e-4 2.46e-3 ✓ sig.
Transcriptional misregulation in cancer
SPI1, TCF3, MYC, PBX1, RUNX1
 KEGG 5 / 198 10.1× 1.18e-4 2.56e-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
SLC39A7, CD79A, BLNK, CD79B, PIK3R1, TCF3, PIK3CD
 GO:0030183 7 / 80 54.5× 3.79e-11 1.20e-8 ✓ sig.
B cell receptor signaling pathway
CD79A, BLNK, CD79B, PIK3CD
 GO:0050853 4 / 56 44.5× 1.87e-6 1.36e-4 ✓ sig.
positive regulation of DNA-templated transcription
SPI1, TCF3, ARID1A, MLLT11, MYC, RET, SMARCA4, RUNX1
 GO:0045893 8 / 778 6.4× 2.25e-5 9.86e-4 ✓ sig.
transcription initiation-coupled chromatin remodeling
SPI1, ARID1A, SMARCA4
 GO:0045815 3 / 41 45.6× 3.82e-5 1.47e-3 ✓ sig.
B cell activation
CD79A, BLNK, PIK3CD
 GO:0042113 3 / 44 42.5× 4.73e-5 1.72e-3 ✓ sig.
myeloid leukocyte differentiation
SPI1, RUNX1
 GO:0002573 2 / 7 178× 5.21e-5 1.86e-3 ✓ sig.
positive regulation of myoblast differentiation
LRRC8A, ARID1A, SMARCA4
 GO:0045663 3 / 47 39.8× 5.77e-5 2.00e-3 ✓ sig.
germinal center B cell differentiation
POU2AF1, SPI1
 GO:0002314 2 / 9 138× 8.91e-5 2.78e-3 ✓ sig.
positive regulation of miRNA transcription
SPI1, MYC, SMARCA4
 GO:1902895 3 / 56 33.4× 9.77e-5 2.97e-3 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
TCF3, ARID1A, SMARCA4
 GO:2000045 3 / 57 32.8× 1.03e-4 3.09e-3 ✓ sig.
fibroblast apoptotic process
BBC3, MYC
 GO:0044346 2 / 11 113× 1.36e-4 3.80e-3 ✓ sig.
immune response
TNFSF13, IGLL1, CD79B, PIK3R1, PIK3CD, HLA-DQA1
 GO:0006955 6 / 543 6.9× 1.92e-4 4.91e-3 ✓ sig.
regulation of multicellular organismal development
PIK3CD, RUNX1
 GO:2000026 2 / 15 83.1× 2.58e-4 6.05e-3 ✓ sig.
positive regulation of developmental process
PIK3CD, RUNX1
 GO:0051094 2 / 16 77.9× 2.95e-4 6.63e-3 ✓ sig.
natural killer cell differentiation
PIK3CD, PBX1
 GO:0001779 2 / 19 65.6× 4.19e-4 8.50e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Agammaglobulinemia Burkitt lymphoma 0.065 2 1.12e-4 3.90e-4 ✓ sig.
Agammaglobulinemia agammaglobulinemia 10, autosomal dominant 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Agammaglobulinemia agammaglobulinemia 2, autosomal recessive 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Agammaglobulinemia agammaglobulinemia 3, autosomal recessive 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Agammaglobulinemia agammaglobulinemia 4, autosomal recessive 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Agammaglobulinemia agammaglobulinemia 6, autosomal recessive 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Agammaglobulinemia autosomal agammaglobulinemia 0.071 1 8.44e-4 1.48e-3 ✓ sig.
autosomal agammaglobulinemia Burkitt lymphoma 0.050 1 1.23e-3 1.97e-3 ✓ sig.