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 99

12 diseases · 25 shared-gene connections
12 Diseases
26 Unique genes
0.272 Avg. similarity score
Chromosome 17q23.1-q23.2 deletion syndrome 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 ⇵
Chromosome 17q23.1-q23.2 deletion syndrome 7 7 1
Epilepsy with myoclonic absence 7 7 1
Glucose transporter type 1 deficiency syndrome 7 7 1
Epilepsy with myoclonic atonic seizures 6 6 7
GLUT1 deficiency syndrome 5 5 1
Intraductal noninfiltrating carcinoma 5 5 5
Cryohydrocytosis 4 4 2
Choreoathetosis 3 3 6
Anaplasia 2 2 2
Ductal carcinoma 2 2 11
Bladder disease 1 1 3
Intellectual developmental disorder seizures epilepsy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SLC2A1 9 / 12 Choreoathetosis, Chromosome 17q23.1-q23.2 deletion syndrome, Cryohydrocytosis, Ductal carcinoma and 5 more
CA9 3 / 12 Anaplasia, Ductal carcinoma, Intraductal noninfiltrating carcinoma
HIF1A 3 / 12 Anaplasia, Ductal carcinoma, Intraductal noninfiltrating carcinoma
AP2M1 2 / 12 Epilepsy with myoclonic atonic seizures, Intellectual developmental disorder seizures epilepsy
SLC6A1 2 / 12 Bladder disease, Epilepsy with myoclonic atonic seizures
STAT5A 2 / 12 Ductal carcinoma, Intraductal noninfiltrating carcinoma
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 ⇵
Central carbon metabolism in cancer
HIF1A, MYC, PTEN, SLC2A1, TP53, LDHB
 KEGG 6 / 71 39.0× 7.22e-9 6.59e-7 ✓ sig.
Endometrial cancer
CDH1, MYC, PTEN, TP53
 KEGG 4 / 59 31.3× 7.24e-6 2.56e-4 ✓ sig.
Thyroid cancer
CDH1, MYC, TP53
 KEGG 3 / 37 37.5× 6.67e-5 1.61e-3 ✓ sig.
Bladder cancer
CDH1, MYC, TP53
 KEGG 3 / 41 33.8× 9.09e-5 2.08e-3 ✓ sig.
Pathways in cancer
HIF1A, CDH1, MYC, PTEN, SLC2A1, STAT5A, TP53
 KEGG 7 / 533 6.1× 1.03e-4 2.30e-3 ✓ sig.
Human T-cell leukemia virus 1 infection
MYC, PTEN, SLC2A1, STAT5A, TP53
 KEGG 5 / 224 10.3× 1.03e-4 2.31e-3 ✓ sig.
Thyroid hormone signaling pathway
HIF1A, MYC, SLC2A1, TP53
 KEGG 4 / 122 15.1× 1.27e-4 2.73e-3 ✓ sig.
Regulation of gene expression by Hypoxia-inducible Factor
CA9, HIF1A
 Reactome 2 / 11 84.0× 2.45e-4 4.58e-3 ✓ sig.
Melanoma
CDH1, PTEN, TP53
 KEGG 3 / 73 19.0× 5.07e-4 8.04e-3 ✓ sig.
Chronic myeloid leukemia
MYC, STAT5A, TP53
 KEGG 3 / 77 18.0× 5.92e-4 9.10e-3 ✓ sig.
Small cell lung cancer
MYC, PTEN, TP53
 KEGG 3 / 93 14.9× 1.03e-3 1.38e-2 ✓ sig.
Ub-specific processing proteases
HIF1A, MYC, PTEN, TP53
 Reactome 4 / 220 8.4× 1.19e-3 1.55e-2 ✓ sig.
Human cytomegalovirus infection
BCAR1, MYC, TP53, GNAO1
 KEGG 4 / 226 8.2× 1.32e-3 1.67e-2 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
HIF1A, MYC, TP53
 Reactome 3 / 108 12.8× 1.58e-3 1.92e-2 ✓ sig.
HIF-1 signaling pathway
HIF1A, SLC2A1, LDHB
 KEGG 3 / 110 12.6× 1.67e-3 2.00e-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 ⇵
positive regulation of miRNA transcription
HIF1A, FOXA1, MYC, TP53
 GO:1902895 4 / 56 51.3× 1.03e-6 8.50e-5 ✓ sig.
regulation of thymocyte apoptotic process
HIF1A, TP53
 GO:0070243 2 / 2 719× 1.86e-6 1.36e-4 ✓ sig.
negative regulation of epithelial to mesenchymal transition
FOXA1, PTEN, NKX2-1
 GO:0010719 3 / 53 40.7× 5.35e-5 1.89e-3 ✓ sig.
visual learning
HIF1A, HRH1, SYNGAP1
 GO:0008542 3 / 54 39.9× 5.66e-5 1.97e-3 ✓ sig.
prostate gland epithelium morphogenesis
FOXA1, STAT5A
 GO:0060740 2 / 10 144× 8.32e-5 2.64e-3 ✓ sig.
lactate metabolic process
HIF1A, LDHB
 GO:0006089 2 / 10 144× 8.32e-5 2.64e-3 ✓ sig.
negative regulation of axonogenesis
PTEN, SYNGAP1
 GO:0050771 2 / 12 120× 1.22e-4 3.51e-3 ✓ sig.
neuron apoptotic process
HIF1A, TP53, SYNGAP1
 GO:0051402 3 / 98 22.0× 3.33e-4 7.21e-3 ✓ sig.
locomotory behavior
PTEN, GNAO1, NKX2-1
 GO:0007626 3 / 99 21.8× 3.43e-4 7.37e-3 ✓ sig.
epithelial tube branching involved in lung morphogenesis
FOXA1, NKX2-1
 GO:0060441 2 / 20 71.9× 3.48e-4 7.43e-3 ✓ sig.
response to xenobiotic stimulus
CA9, CDH1, MYC, TP53
 GO:0009410 4 / 248 11.6× 3.60e-4 7.59e-3 ✓ sig.
hematopoietic stem cell differentiation
TP53, CHD2
 GO:0060218 2 / 21 68.5× 3.85e-4 7.98e-3 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN8A, SCN1A
 GO:0086002 2 / 24 59.9× 5.04e-4 9.63e-3 ✓ sig.
intrinsic apoptotic signaling pathway by p53 class mediator
ZNF385B, TP53
 GO:0072332 2 / 29 49.6× 7.38e-4 1.24e-2 ✓ sig.
pituitary gland development
CDH1, NKX2-1
 GO:0021983 2 / 30 47.9× 7.91e-4 1.30e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Ductal carcinoma Intraductal noninfiltrating carcinoma 0.308 4 7.04e-13 9.12e-12 ✓ sig.
Anaplasia Intraductal noninfiltrating carcinoma 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Anaplasia Ductal carcinoma 0.167 2 4.64e-7 3.06e-6 ✓ sig.
Glucose transporter type 1 deficiency syndrome GLUT1 deficiency syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Epilepsy with myoclonic absence GLUT1 deficiency syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Epilepsy with myoclonic absence Glucose transporter type 1 deficiency syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Glucose transporter type 1 deficiency syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Epilepsy with myoclonic absence 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome GLUT1 deficiency syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cryohydrocytosis GLUT1 deficiency syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cryohydrocytosis Epilepsy with myoclonic absence 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cryohydrocytosis Glucose transporter type 1 deficiency syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Cryohydrocytosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Intraductal noninfiltrating carcinoma 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Glucose transporter type 1 deficiency syndrome Intraductal noninfiltrating carcinoma 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Epilepsy with myoclonic absence Intraductal noninfiltrating carcinoma 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Choreoathetosis Epilepsy with myoclonic absence 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Choreoathetosis Glucose transporter type 1 deficiency syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Choreoathetosis Chromosome 17q23.1-q23.2 deletion syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Chromosome 17q23.1-q23.2 deletion syndrome Epilepsy with myoclonic atonic seizures 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Glucose transporter type 1 deficiency syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Epilepsy with myoclonic absence Epilepsy with myoclonic atonic seizures 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures GLUT1 deficiency syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Epilepsy with myoclonic atonic seizures Intellectual developmental disorder seizures epilepsy 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Bladder disease Epilepsy with myoclonic atonic seizures 0.100 1 1.36e-3 2.13e-3 ✓ sig.