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 23

24 diseases · 79 shared-gene connections
24 Diseases
21 Unique genes
0.355 Avg. similarity score
Atypical multiple mole melanoma syndrome Most-connected disease (17 links)
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Disease Searched: Duodenal gastrin-producing neuroendocrine tumor 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 ⇵
Atypical multiple mole melanoma syndrome 17 17 1
Trisomy 17 17 1
Vulvar lichen sclerosus 17 17 2
Dysplasia 13 13 1
Mouth mucous membrane leukoplakia 8 8 1
Brain stem neoplasms 7 7 4
Melanoma, cutaneous malignant 7 7 3
Melanoma-pancreatic cancer syndrome 7 7 2
Clear cell chondrosarcoma 6 6 2
Li-fraumeni syndrome 6 6 5
Duodenal gastrin-producing neuroendocrine tumor 5 5 2
Melanoma and neural system tumor syndrome 5 5 1
Melanoma, cutaneous malignant, 2 5 5 1
Melanoma, cutaneous malignant, susceptibility to, 2 5 5 1
Pancreatic gastrinoma 5 5 2
Undifferentiated ovarian carcinoma 5 5 3
Cutaneous malignant melanoma 3 4 4 1
Intestinal cancer 4 4 7
Melanoma, cutaneous malignant, susceptibility to, 3 4 4 1
Neuroepithelial neoplasm 4 4 2
Bryant-li-bhoj neurodevelopmental syndrome 3 3 2
Hemiparkinsonism hemiatrophy syndrome 2 2 1
Iatrogenic kaposi's sarcoma 1 1 3
Mental retardation, autosomal dominant 12 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CDKN2A 18 / 24 Atypical multiple mole melanoma syndrome, Brain stem neoplasms, Clear cell chondrosarcoma, Duodenal gastrin-producing neuroendocrine tumor and 14 more
CDK4 5 / 24 Brain stem neoplasms, Cutaneous malignant melanoma 3, Melanoma, cutaneous malignant, Melanoma, cutaneous malignant, susceptibility to, 3 and 1 more
H3-3B 3 / 24 Bryant-li-bhoj neurodevelopmental syndrome, Clear cell chondrosarcoma, Hemiparkinsonism hemiatrophy syndrome
TP53 3 / 24 Intestinal cancer, Li-fraumeni syndrome, Vulvar lichen sclerosus
ARID1B 2 / 24 Mental retardation, autosomal dominant 12, Undifferentiated ovarian carcinoma
CHEK2 2 / 24 Iatrogenic kaposi's sarcoma, Li-fraumeni syndrome
H3-3A 2 / 24 Bryant-li-bhoj neurodevelopmental syndrome, Neuroepithelial neoplasm
MEN1 2 / 24 Duodenal gastrin-producing neuroendocrine tumor, Pancreatic gastrinoma
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 ⇵
Hepatocellular carcinoma
CDK4, CDK6, CDKN2A, TP53, SMARCA4, ARID2, KRAS, BRAF, ARID1B, PBRM1
 KEGG 10 / 170 33.6× 7.63e-14 1.83e-11 ✓ sig.
Melanoma
CDK4, CDK6, CDKN2A, MDM2, TP53, KRAS, BRAF, MITF
 KEGG 8 / 73 62.7× 2.40e-13 5.14e-11 ✓ sig.
p53 signaling pathway
CDK4, CDK6, CDKN2A, PPM1D, CHEK2, MDM2, TP53
 KEGG 7 / 75 53.4× 3.02e-11 4.11e-9 ✓ sig.
Glioma
CDK4, CDK6, CDKN2A, MDM2, TP53, KRAS, BRAF
 KEGG 7 / 76 52.7× 3.32e-11 4.45e-9 ✓ sig.
Chronic myeloid leukemia
CDK4, CDK6, CDKN2A, MDM2, TP53, KRAS, BRAF
 KEGG 7 / 77 52.0× 3.65e-11 4.86e-9 ✓ sig.
Bladder cancer
CDK4, CDKN2A, MDM2, TP53, KRAS, BRAF
 KEGG 6 / 41 83.7× 5.65e-11 7.10e-9 ✓ sig.
Oxidative Stress Induced Senescence
CDK4, CDK6, CDKN2A, H3-3A, H3-3B, MDM2, TP53
 Reactome 7 / 125 32.0× 1.15e-9 1.05e-7 ✓ sig.
Non-small cell lung cancer
CDK4, CDK6, CDKN2A, TP53, KRAS, BRAF
 KEGG 6 / 73 47.0× 2.07e-9 1.78e-7 ✓ sig.
Oncogene Induced Senescence
CDK4, CDK6, CDKN2A, MDM2, TP53
 Reactome 5 / 33 86.7× 2.25e-9 1.93e-7 ✓ sig.
Stabilization of p53
CDKN2A, CHEK2, MDM2, TP53
 Reactome 4 / 11 208× 2.26e-9 1.94e-7 ✓ sig.
Pancreatic cancer
CDK4, CDK6, CDKN2A, TP53, KRAS, BRAF
 KEGG 6 / 77 44.6× 2.86e-9 2.41e-7 ✓ sig.
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6
CDK4, CDK6, CDKN2A
 Reactome 3 / 3 572× 4.61e-9 3.69e-7 ✓ sig.
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6
CDK4, CDK6, CDKN2A
 Reactome 3 / 3 572× 4.61e-9 3.69e-7 ✓ sig.
Cellular senescence
CDK4, CDK6, CDKN2A, CHEK2, MDM2, TP53, KRAS
 KEGG 7 / 157 25.5× 5.69e-9 4.47e-7 ✓ sig.
Endocrine resistance
CDK4, CDKN2A, MDM2, TP53, KRAS, BRAF
 KEGG 6 / 99 34.7× 1.32e-8 9.51e-7 ✓ 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 double-strand break repair
WRAP53, SMARCA4, ARID2, ARID1B, PBRM1
 GO:2000781 5 / 47 94.7× 1.60e-9 3.50e-7 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
CDKN2A, SMARCA4, ARID2, ARID1B, PBRM1
 GO:2000045 5 / 57 78.1× 4.33e-9 8.40e-7 ✓ sig.
regulation of G0 to G1 transition
SMARCA4, ARID2, ARID1B, PBRM1
 GO:0070316 4 / 25 142× 1.47e-8 2.47e-6 ✓ sig.
regulation of nucleotide-excision repair
SMARCA4, ARID2, ARID1B, PBRM1
 GO:2000819 4 / 28 127× 2.37e-8 3.74e-6 ✓ sig.
regulation of mitotic metaphase/anaphase transition
SMARCA4, ARID2, ARID1B, PBRM1
 GO:0030071 4 / 34 105× 5.35e-8 7.52e-6 ✓ sig.
positive regulation of T cell differentiation
SMARCA4, ARID2, ARID1B, PBRM1
 GO:0045582 4 / 40 89.0× 1.05e-7 1.32e-5 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, SMARCA4, MEN1, ARID1B
 GO:0045815 4 / 41 86.8× 1.16e-7 1.44e-5 ✓ sig.
positive regulation of myoblast differentiation
SMARCA4, ARID2, ARID1B, PBRM1
 GO:0045663 4 / 47 75.7× 2.04e-7 2.30e-5 ✓ sig.
DNA damage response, signal transduction by p53 class mediator
PPM1D, CHEK2, MDM2, TP53
 GO:0030330 4 / 48 74.2× 2.22e-7 2.47e-5 ✓ sig.
negative regulation of cell population proliferation
CDK6, CDKN2A, PPM1D, TP53, ARID2, MEN1, PBRM1
 GO:0008285 7 / 444 14.0× 3.55e-7 3.66e-5 ✓ sig.
replicative senescence
CDKN2A, CHEK2, TP53
 GO:0090399 3 / 16 167× 6.79e-7 6.26e-5 ✓ sig.
positive regulation of gene expression
CDK6, CDKN2A, MDM2, TP53, KRAS, BRAF, MITF
 GO:0010628 7 / 504 12.4× 8.34e-7 7.40e-5 ✓ sig.
negative regulation of chromosome condensation
H3-3A, H3-3B
 GO:1902340 2 / 2 890× 1.20e-6 9.99e-5 ✓ sig.
positive regulation of cell differentiation
SMARCA4, ARID2, ARID1B, PBRM1
 GO:0045597 4 / 83 42.9× 2.04e-6 1.54e-4 ✓ sig.
response to gamma radiation
CHEK2, TP53, MEN1
 GO:0010332 3 / 27 98.9× 3.52e-6 2.39e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Duodenal gastrin-producing neuroendocrine tumor Pancreatic gastrinoma 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Melanoma-pancreatic cancer syndrome Melanoma, cutaneous malignant 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Brain stem neoplasms Melanoma-pancreatic cancer syndrome 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Brain stem neoplasms Melanoma, cutaneous malignant 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Dysplasia Melanoma, cutaneous malignant, susceptibility to, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dysplasia Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dysplasia Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dysplasia Melanoma and neural system tumor syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mouth mucous membrane leukoplakia Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mouth mucous membrane leukoplakia Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma and neural system tumor syndrome Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma and neural system tumor syndrome Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma and neural system tumor syndrome Mouth mucous membrane leukoplakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, susceptibility to, 2 Mouth mucous membrane leukoplakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dysplasia Mouth mucous membrane leukoplakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, susceptibility to, 2 Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Melanoma, cutaneous malignant, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, 2 Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, 2 Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Dysplasia Melanoma, cutaneous malignant, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, 2 Mouth mucous membrane leukoplakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Melanoma, cutaneous malignant, susceptibility to, 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, cutaneous malignant, susceptibility to, 2 Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Mouth mucous membrane leukoplakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Melanoma and neural system tumor syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Trisomy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Trisomy Vulvar lichen sclerosus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cutaneous malignant melanoma 3 Melanoma, cutaneous malignant, susceptibility to, 3 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Duodenal gastrin-producing neuroendocrine tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanoma-pancreatic cancer syndrome Melanoma, cutaneous malignant, susceptibility to, 3 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Clear cell chondrosarcoma Vulvar lichen sclerosus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Clear cell chondrosarcoma Trisomy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Clear cell chondrosarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Clear cell chondrosarcoma Hemiparkinsonism hemiatrophy syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Melanoma-pancreatic cancer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanoma-pancreatic cancer syndrome Trisomy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Melanoma-pancreatic cancer syndrome Vulvar lichen sclerosus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bryant-li-bhoj neurodevelopmental syndrome Hemiparkinsonism hemiatrophy syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Duodenal gastrin-producing neuroendocrine tumor Trisomy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Clear cell chondrosarcoma Dysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Neuroepithelial neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neuroepithelial neoplasm Trisomy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neuroepithelial neoplasm Vulvar lichen sclerosus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Pancreatic gastrinoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pancreatic gastrinoma Trisomy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cutaneous malignant melanoma 3 Melanoma-pancreatic cancer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Duodenal gastrin-producing neuroendocrine tumor Vulvar lichen sclerosus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Duodenal gastrin-producing neuroendocrine tumor Dysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pancreatic gastrinoma Vulvar lichen sclerosus 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Dysplasia Pancreatic gastrinoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Undifferentiated ovarian carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Undifferentiated ovarian carcinoma Vulvar lichen sclerosus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Trisomy Undifferentiated ovarian carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysplasia Undifferentiated ovarian carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Melanoma, cutaneous malignant Melanoma, cutaneous malignant, susceptibility to, 3 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Mental retardation, autosomal dominant 12 Undifferentiated ovarian carcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Melanoma, cutaneous malignant Trisomy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Melanoma, cutaneous malignant 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Melanoma, cutaneous malignant Vulvar lichen sclerosus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cutaneous malignant melanoma 3 Melanoma, cutaneous malignant 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bryant-li-bhoj neurodevelopmental syndrome Clear cell chondrosarcoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Bryant-li-bhoj neurodevelopmental syndrome Neuroepithelial neoplasm 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Brain stem neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain stem neoplasms Trisomy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain stem neoplasms Vulvar lichen sclerosus 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain stem neoplasms Cutaneous malignant melanoma 3 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Li-fraumeni syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Li-fraumeni syndrome Trisomy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Li-fraumeni syndrome Vulvar lichen sclerosus 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain stem neoplasms Melanoma, cutaneous malignant, susceptibility to, 3 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysplasia Li-fraumeni syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Li-fraumeni syndrome Mouth mucous membrane leukoplakia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Intestinal cancer Vulvar lichen sclerosus 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Intestinal cancer Trisomy 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Intestinal cancer 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Dysplasia Intestinal cancer 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Iatrogenic kaposi's sarcoma Li-fraumeni syndrome 0.167 1 5.16e-4 9.13e-4 ✓ sig.