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 310

7 diseases · 16 shared-gene connections
7 Diseases
14 Unique genes
0.270 Avg. similarity score
Ataxia telangiectasia Most-connected disease (6 links)
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Disease Searched: Albright hereditary osteodystrophy type 3 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 ⇵
Ataxia telangiectasia 6 6 11
2q37 microdeletion syndrome 5 5 1
Albright hereditary osteodystrophy type 3 5 5 1
Chromosome 2q37 deletion syndrome 5 5 4
Del(2)(q37) 5 5 1
Neurodevelopmental disorder with central hypotonia and dysmorphic facies 5 5 1
Intracranial germ cell tumor 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HDAC4 6 / 7 2q37 microdeletion syndrome, Albright hereditary osteodystrophy type 3, Ataxia telangiectasia, Chromosome 2q37 deletion syndrome and 2 more
BAK1 2 / 7 Ataxia telangiectasia, Intracranial germ cell tumor
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 ⇵
Thyroid cancer
BAK1, BAX, BRAF
 KEGG 3 / 37 69.6× 9.57e-6 2.81e-4 ✓ sig.
Release of apoptotic factors from the mitochondria
BAK1, BAX
 Reactome 2 / 5 343× 1.26e-5 3.53e-4 ✓ sig.
Sensing of DNA Double Strand Breaks
ATM, MRE11
 Reactome 2 / 6 286× 1.89e-5 4.97e-4 ✓ sig.
HDR through Homologous Recombination (HRR)
ATM, MRE11, PCNA
 Reactome 3 / 48 53.6× 2.11e-5 5.46e-4 ✓ sig.
Hepatitis C
BAK1, BAX, BRAF, IFNG
 KEGG 4 / 159 21.6× 2.67e-5 6.60e-4 ✓ sig.
Endometrial cancer
BAK1, BAX, BRAF
 KEGG 3 / 59 43.6× 3.94e-5 9.05e-4 ✓ sig.
RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs)
IFNG, IL2
 Reactome 2 / 10 172× 5.65e-5 1.20e-3 ✓ sig.
Melanoma
BAK1, BAX, BRAF
 KEGG 3 / 73 35.3× 7.47e-5 1.50e-3 ✓ sig.
Non-small cell lung cancer
BAK1, BAX, BRAF
 KEGG 3 / 73 35.3× 7.47e-5 1.50e-3 ✓ sig.
Platinum drug resistance
ATM, BAK1, BAX
 KEGG 3 / 75 34.3× 8.10e-5 1.60e-3 ✓ sig.
Glioma
BAK1, BAX, BRAF
 KEGG 3 / 76 33.9× 8.43e-5 1.66e-3 ✓ sig.
Pancreatic cancer
BAK1, BAX, BRAF
 KEGG 3 / 77 33.4× 8.77e-5 1.71e-3 ✓ sig.
Chronic myeloid leukemia
BAK1, BAX, BRAF
 KEGG 3 / 77 33.4× 8.77e-5 1.71e-3 ✓ sig.
Colorectal cancer
BAK1, BAX, BRAF
 KEGG 3 / 87 29.6× 1.26e-4 2.28e-3 ✓ sig.
Endocrine resistance
BAX, BIK, BRAF
 KEGG 3 / 99 26.0× 1.85e-4 3.09e-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 ⇵
positive regulation of protein-containing complex assembly
BAK1, BAX, BIK, IFNG
 GO:0031334 4 / 50 107× 4.45e-8 6.42e-6 ✓ sig.
B cell negative selection
BAK1, BAX
 GO:0002352 2 / 2 1,335× 5.21e-7 5.04e-5 ✓ sig.
positive regulation of release of cytochrome c from mitochondria
BAK1, BAX, BIK
 GO:0090200 3 / 25 160× 7.62e-7 6.87e-5 ✓ sig.
extrinsic apoptotic signaling pathway in absence of ligand
BAK1, BAX, IL2
 GO:0097192 3 / 36 111× 2.36e-6 1.73e-4 ✓ sig.
post-embryonic camera-type eye morphogenesis
BAK1, BAX
 GO:0048597 2 / 4 667× 3.12e-6 2.17e-4 ✓ sig.
apoptotic process involved in blood vessel morphogenesis
BAK1, BAX
 GO:1902262 2 / 5 534× 5.21e-6 3.27e-4 ✓ sig.
negative regulation of endoplasmic reticulum calcium ion concentration
BAK1, BAX
 GO:0032471 2 / 6 445× 7.80e-6 4.51e-4 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage
ATM, BAK1, BAX
 GO:0008630 3 / 54 74.2× 8.12e-6 4.64e-4 ✓ sig.
cellular response to UV
BAK1, BAX, PCNA
 GO:0034644 3 / 55 72.8× 8.58e-6 4.84e-4 ✓ sig.
positive regulation of IRE1-mediated unfolded protein response
BAK1, BAX
 GO:1903896 2 / 8 334× 1.46e-5 7.28e-4 ✓ sig.
regulation of apoptotic signaling pathway
BAK1, BAX
 GO:2001233 2 / 9 297× 1.87e-5 8.78e-4 ✓ sig.
leukocyte homeostasis
BAK1, BAX
 GO:0001776 2 / 9 297× 1.87e-5 8.78e-4 ✓ sig.
vagina development
BAK1, BAX
 GO:0060068 2 / 10 267× 2.34e-5 1.04e-3 ✓ sig.
establishment or maintenance of transmembrane electrochemical gradient
BAK1, BAX
 GO:0010248 2 / 11 243× 2.86e-5 1.20e-3 ✓ sig.
thymocyte apoptotic process
BAK1, BAX
 GO:0070242 2 / 11 243× 2.86e-5 1.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
2q37 microdeletion syndrome Albright hereditary osteodystrophy type 3 0.500 1 6.46e-5 1.98e-4 ✓ sig.
2q37 microdeletion syndrome Del(2)(q37) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
2q37 microdeletion syndrome Neurodevelopmental disorder with central hypotonia and dysmorphic facies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Albright hereditary osteodystrophy type 3 Del(2)(q37) 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Albright hereditary osteodystrophy type 3 Neurodevelopmental disorder with central hypotonia and dysmorphic facies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Del(2)(q37) Neurodevelopmental disorder with central hypotonia and dysmorphic facies 0.500 1 6.46e-5 1.98e-4 ✓ sig.
2q37 microdeletion syndrome Chromosome 2q37 deletion syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Albright hereditary osteodystrophy type 3 Chromosome 2q37 deletion syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Chromosome 2q37 deletion syndrome Del(2)(q37) 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Chromosome 2q37 deletion syndrome Neurodevelopmental disorder with central hypotonia and dysmorphic facies 0.200 1 2.58e-4 5.38e-4 ✓ sig.
2q37 microdeletion syndrome Ataxia telangiectasia 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Albright hereditary osteodystrophy type 3 Ataxia telangiectasia 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Ataxia telangiectasia Del(2)(q37) 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Ataxia telangiectasia Neurodevelopmental disorder with central hypotonia and dysmorphic facies 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Ataxia telangiectasia Intracranial germ cell tumor 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Ataxia telangiectasia Chromosome 2q37 deletion syndrome 0.071 1 2.58e-3 3.34e-3 ✓ sig.