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

10 diseases · 34 shared-gene connections
10 Diseases
12 Unique genes
0.353 Avg. similarity score
Deafness-lymphedema-leukemia syndrome Most-connected disease (9 links)
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Disease Searched: Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency 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 ⇵
Deafness-lymphedema-leukemia syndrome 9 9 1
Emberger syndrome 9 9 1
Gata2 deficiency 9 9 1
Lymphedema, primary, with myelodysplasia 9 9 1
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency 7 7 1
Leukemia, acute myeloid, susceptibility to 5 5 2
Malignant biphasic mesothelioma 5 5 4
Monocytopenia with susceptibility to infections 5 5 1
Primary graft dysfunction 5 5 4
Vascular remodeling 5 5 6

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

Gene ⇵ Member diseases ⇵ Linked diseases
GATA2 10 / 10 Deafness-lymphedema-leukemia syndrome, Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency, Emberger syndrome, Gata2 deficiency and 6 more
SENP1 2 / 10 Primary graft dysfunction, Vascular remodeling
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 ⇵
Stabilization of p53
TP53, CDKN2A
 Reactome 2 / 11 182× 5.01e-5 1.09e-3 ✓ sig.
SUMOylation of transcription factors
TP53, CDKN2A
 Reactome 2 / 18 111× 1.39e-4 2.46e-3 ✓ sig.
Oncogene Induced Senescence
TP53, CDKN2A
 Reactome 2 / 33 60.7× 4.75e-4 6.42e-3 ✓ sig.
Regulation of TP53 Degradation
TP53, CDKN2A
 Reactome 2 / 36 55.6× 5.66e-4 7.36e-3 ✓ sig.
Transcriptional Regulation by VENTX
TP53, CDKN2A
 Reactome 2 / 38 52.7× 6.31e-4 7.99e-3 ✓ sig.
Bladder cancer
TP53, CDKN2A
 KEGG 2 / 41 48.8× 7.34e-4 8.97e-3 ✓ sig.
Evasion of Oncogene Induced Senescence Due to p14ARF Defects
CDKN2A
 Reactome 1 / 1 1,001× 9.99e-4 1.13e-2 ✓ sig.
Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects
CDKN2A
 Reactome 1 / 1 1,001× 9.99e-4 1.13e-2 ✓ sig.
Malaria
SELP, VCAM1
 KEGG 2 / 50 40.0× 1.09e-3 1.21e-2 ✓ sig.
Lipid and atherosclerosis
SELP, VCAM1, TP53
 KEGG 3 / 216 13.9× 1.12e-3 1.23e-2 ✓ sig.
Human cytomegalovirus infection
CXCR2, TP53, CDKN2A
 KEGG 3 / 226 13.3× 1.28e-3 1.37e-2 ✓ sig.
Pathways in cancer
AGT, FLT3, TP53, CDKN2A
 KEGG 4 / 533 7.5× 1.43e-3 1.48e-2 ✓ sig.
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4
CDKN2A
 Reactome 1 / 2 500× 2.00e-3 1.90e-2 ✓ sig.
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4
CDKN2A
 Reactome 1 / 2 500× 2.00e-3 1.90e-2 ✓ sig.
Apoptotic factor-mediated response
CDKN2A
 Reactome 1 / 2 500× 2.00e-3 1.90e-2 ✓ 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 cell growth
ACVRL1, GJA1, TP53, CDKN2A
 GO:0030308 4 / 115 54.2× 6.49e-7 6.04e-5 ✓ sig.
positive regulation of miRNA transcription
GATA2, AGT, TP53
 GO:1902895 3 / 56 83.4× 5.50e-6 3.42e-4 ✓ sig.
common myeloid progenitor cell proliferation
FLT3, BAP1
 GO:0035726 2 / 9 346× 1.36e-5 6.89e-4 ✓ sig.
negative regulation of neuroblast proliferation
GATA2, TP53
 GO:0007406 2 / 14 222× 3.43e-5 1.39e-3 ✓ sig.
rRNA transcription
TP53, CDKN2A
 GO:0009303 2 / 15 208× 3.95e-5 1.54e-3 ✓ sig.
replicative senescence
TP53, CDKN2A
 GO:0090399 2 / 16 195× 4.51e-5 1.71e-3 ✓ sig.
negative regulation of gene expression
GATA2, ACVRL1, AGT, TP53
 GO:0010629 4 / 339 18.4× 4.69e-5 1.77e-3 ✓ sig.
leukocyte tethering or rolling
SELP, VCAM1
 GO:0050901 2 / 20 156× 7.14e-5 2.40e-3 ✓ sig.
positive regulation of DNA-templated transcription
GATA2, ACVRL1, AGT, TP53, CDKN2A
 GO:0045893 5 / 778 10.0× 7.66e-5 2.54e-3 ✓ sig.
negative regulation of cell population proliferation
ACVRL1, BAP1, TP53, CDKN2A
 GO:0008285 4 / 444 14.0× 1.34e-4 3.80e-3 ✓ sig.
hematopoietic stem cell homeostasis
GATA2, BAP1
 GO:0061484 2 / 30 104× 1.63e-4 4.38e-3 ✓ sig.
leukocyte cell-cell adhesion
SELP, VCAM1
 GO:0007159 2 / 33 94.4× 1.97e-4 5.03e-3 ✓ sig.
positive regulation of reactive oxygen species metabolic process
AGT, TP53
 GO:2000379 2 / 34 91.6× 2.10e-4 5.25e-3 ✓ sig.
positive regulation of gene expression
GATA2, GJA1, TP53, CDKN2A
 GO:0010628 4 / 504 12.4× 2.18e-4 5.39e-3 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
SELP, AGT, FLT3
 GO:0051897 3 / 217 21.5× 3.14e-4 7.02e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Primary graft dysfunction Vascular remodeling 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Emberger syndrome Gata2 deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Gata2 deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lymphedema, primary, with myelodysplasia Monocytopenia with susceptibility to infections 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gata2 deficiency Monocytopenia with susceptibility to infections 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gata2 deficiency Lymphedema, primary, with myelodysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Emberger syndrome Monocytopenia with susceptibility to infections 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Emberger syndrome Lymphedema, primary, with myelodysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Monocytopenia with susceptibility to infections 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Lymphedema, primary, with myelodysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Emberger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Gata2 deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Monocytopenia with susceptibility to infections 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Lymphedema, primary, with myelodysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Emberger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Leukemia, acute myeloid, susceptibility to Lymphedema, primary, with myelodysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Leukemia, acute myeloid, susceptibility to 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Emberger syndrome Leukemia, acute myeloid, susceptibility to 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gata2 deficiency Leukemia, acute myeloid, susceptibility to 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Leukemia, acute myeloid, susceptibility to 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Malignant biphasic mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gata2 deficiency Malignant biphasic mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Emberger syndrome Malignant biphasic mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Lymphedema, primary, with myelodysplasia Malignant biphasic mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dendritic cell, monocyte, b lymphocyte, and natural killer lymphocyte deficiency Malignant biphasic mesothelioma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Primary graft dysfunction 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Gata2 deficiency Primary graft dysfunction 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Emberger syndrome Primary graft dysfunction 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Lymphedema, primary, with myelodysplasia Primary graft dysfunction 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Deafness-lymphedema-leukemia syndrome Vascular remodeling 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Gata2 deficiency Vascular remodeling 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Emberger syndrome Vascular remodeling 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Lymphedema, primary, with myelodysplasia Vascular remodeling 0.143 1 3.87e-4 7.33e-4 ✓ sig.