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 45

16 diseases · 28 shared-gene connections
16 Diseases
166 Unique genes
0.191 Avg. similarity score
B-lymphoblastic leukemia/lymphoma Most-connected disease (6 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 ⇵
B-lymphoblastic leukemia/lymphoma 6 6 19
Li-fraumeni syndrome 6 6 5
Vulvar lichen sclerosus 6 6 2
Atypical multiple mole melanoma syndrome 5 5 1
Trisomy 5 5 1
melanoma-pancreatic cancer syndrome 5 5 1
Brain stem neoplasms 4 4 4
Carcinogenesis 4 4 18
Endometrial hyperplasia 4 4 10
B-cell acute lymphoblastic leukemia 3 3 60
Lymphoblastic leukemia 2 2 57
Nasopharyngeal carcinoma 2 2 22
Gestational trophoblastic disease 1 1 1
Intellectual developmental disorder growth other organ 1 1 1
granulocytopenia with immunoglobulin abnormality 1 1 1
leukemia, acute myeloid, susceptibility to 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CDKN2A 11 / 16 Atypical multiple mole melanoma syndrome, B-cell acute lymphoblastic leukemia, B-lymphoblastic leukemia/lymphoma, Brain stem neoplasms and 7 more
TP53 5 / 16 B-lymphoblastic leukemia/lymphoma, Endometrial hyperplasia, Li-fraumeni syndrome, Nasopharyngeal carcinoma and 1 more
FLT3 4 / 16 B-cell acute lymphoblastic leukemia, B-lymphoblastic leukemia/lymphoma, leukemia, acute myeloid, susceptibility to, Lymphoblastic leukemia
GATA3 3 / 16 B-cell acute lymphoblastic leukemia, B-lymphoblastic leukemia/lymphoma, Carcinogenesis
IKZF1 3 / 16 B-cell acute lymphoblastic leukemia, B-lymphoblastic leukemia/lymphoma, Lymphoblastic leukemia
KRAS 3 / 16 Carcinogenesis, Endometrial hyperplasia, Nasopharyngeal carcinoma
PIP4K2A 3 / 16 B-cell acute lymphoblastic leukemia, B-lymphoblastic leukemia/lymphoma, Lymphoblastic leukemia
ABL1 2 / 16 B-lymphoblastic leukemia/lymphoma, Carcinogenesis
ARID5B 2 / 16 B-cell acute lymphoblastic leukemia, Lymphoblastic leukemia
BCR 2 / 16 B-lymphoblastic leukemia/lymphoma, Lymphoblastic leukemia
CEBPE 2 / 16 B-cell acute lymphoblastic leukemia, Lymphoblastic leukemia
ERBB2 2 / 16 Carcinogenesis, Nasopharyngeal carcinoma
GSDMB 2 / 16 B-cell acute lymphoblastic leukemia, Lymphoblastic leukemia
HYOU1 2 / 16 B-cell acute lymphoblastic leukemia, granulocytopenia with immunoglobulin abnormality
LHPP 2 / 16 B-cell acute lymphoblastic leukemia, Lymphoblastic leukemia
PAX5 2 / 16 B-lymphoblastic leukemia/lymphoma, Lymphoblastic leukemia
POU5F1 2 / 16 Carcinogenesis, Gestational trophoblastic disease
PPM1D 2 / 16 Brain stem neoplasms, Intellectual developmental disorder growth other organ
PTEN 2 / 16 Endometrial hyperplasia, Nasopharyngeal carcinoma
TP63 2 / 16 Lymphoblastic leukemia, Nasopharyngeal 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 ⇵
Chronic myeloid leukemia
CDKN2A, KRAS, TP53, BAK1, NFKB1, ABL1, BCR, CDK4, CDK6, AKT1, BRAF, BAX
 KEGG 17 / 77 16.0× 2.56e-16 1.09e-13 ✓ sig.
Melanoma
CDKN2A, KRAS, PTEN, TP53, BAK1, PDGFRA, CDK4, CDK6, AKT1, BRAF, MET, BAX
 KEGG 16 / 73 15.9× 2.28e-15 8.19e-13 ✓ sig.
Glioma
CDKN2A, KRAS, PTEN, TP53, BAK1, PDGFRA, CDK4, CDK6, AKT1, BRAF, BAX, MDM2
 KEGG 15 / 76 14.3× 9.29e-14 2.41e-11 ✓ sig.
Pathways in cancer
APC, CDKN2A, CTNNB1, KRAS, PTEN, TP53, BAK1, CEBPA, FLT3, IL7, NFKB1, STAT4
 KEGG 33 / 533 4.5× 2.42e-13 5.77e-11 ✓ sig.
Endometrial cancer
APC, CTNNB1, KRAS, PTEN, TP53, BAK1, AKT1, BRAF, ERBB2, BAX, AKT2, CCND1
 KEGG 13 / 59 15.9× 9.77e-13 2.14e-10 ✓ sig.
Non-small cell lung cancer
CDKN2A, KRAS, TP53, BAK1, CDK4, CDK6, AKT1, BRAF, ERBB2, MET, BAX, AKT2
 KEGG 14 / 73 13.9× 9.76e-13 2.14e-10 ✓ sig.
Pancreatic cancer
CDKN2A, KRAS, TP53, BAK1, NFKB1, CDK4, CDK6, AKT1, BRAF, ERBB2, BAX, AKT2
 KEGG 14 / 77 13.2× 2.11e-12 4.36e-10 ✓ sig.
Prostate cancer
CTNNB1, KRAS, PTEN, TP53, ERG, NFKB1, PDGFRA, AKT1, BRAF, ERBB2, MDM2, AKT2
 KEGG 15 / 98 11.1× 4.60e-12 8.77e-10 ✓ sig.
Hepatocellular carcinoma
APC, CDKN2A, CTNNB1, KRAS, PTEN, TP53, BAK1, CDK4, CDK6, AKT1, BRAF, MET
 KEGG 18 / 170 7.7× 1.90e-11 3.21e-9 ✓ sig.
Cellular senescence
CDKN2A, KRAS, PTEN, TP53, NFKB1, TRAF3IP2, HLA-C, CDK4, CDK6, AKT1, CDKN2B, NBN
 KEGG 17 / 157 7.8× 4.96e-11 7.63e-9 ✓ sig.
Central carbon metabolism in cancer
KRAS, PTEN, TP53, FLT3, GLS, PDGFRA, AKT1, ERBB2, MET, TIGAR, AKT2, PIK3CA
 KEGG 12 / 71 12.2× 2.06e-10 2.77e-8 ✓ sig.
Human cytomegalovirus infection
CDKN2A, CTNNB1, KRAS, TP53, BAK1, CCL2, NFKB1, PDGFRA, HLA-C, CDK4, CDK6, AKT1
 KEGG 19 / 226 6.1× 2.87e-10 3.73e-8 ✓ sig.
Small cell lung cancer
PTEN, TP53, BAK1, NFKB1, CDK4, CDK6, AKT1, CDKN2B, BAX, AKT2, CCND1, NFKBIA
 KEGG 13 / 93 10.1× 4.18e-10 5.18e-8 ✓ sig.
Endocrine resistance
CDKN2A, KRAS, TP53, CDK4, AKT1, BRAF, ERBB2, BAX, MDM2, AKT2, CCND1, MMP2
 KEGG 13 / 99 9.5× 9.27e-10 1.05e-7 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
CTNNB1, KRAS, TP53, BAK1, CSF2, NFKB1, HLA-C, CDK4, CDK6, AKT1, MAP1LC3B2, BAX
 KEGG 17 / 196 6.3× 1.63e-9 1.72e-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 ⇵
regulation of cell cycle
CDKN1C, CDKN2A, PTEN, TP53, BAK1, CEBPA, IRF1, ABL1, BCR, CDK4, CDK6, BAX
 GO:0051726 18 / 262 7.7× 2.11e-11 7.14e-9 ✓ sig.
positive regulation of transcription by RNA polymerase II
CDKN2A, CTNNB1, PTEN, TP53, CEBPA, CEBPE, ELK3, ERG, GATA3, IKZF3, IRF1, MYB
 GO:0045944 34 / 1,208 3.2× 1.55e-9 3.30e-7 ✓ sig.
negative regulation of cell population proliferation
SH2B3, APC, CDKN2A, CTNNB1, PTEN, TP53, BAK1, CEBPA, GATA3, IRF1, CDK6, PPM1D
 GO:0008285 20 / 444 5.1× 2.78e-9 5.53e-7 ✓ sig.
response to gamma radiation
TP53, BAK1, GATA3, TIGAR, BAX, CHEK2, SOD2
 GO:0010332 7 / 27 29.2× 2.94e-9 5.79e-7 ✓ sig.
regulation of cell population proliferation
CTNNB1, TP53, CEBPA, CSF2, STAT4, STAT6, PBX1, ABL1, CDK6, BRAF, ERBB2, TAL1
 GO:0042127 14 / 201 7.8× 3.31e-9 6.47e-7 ✓ sig.
cell population proliferation
CTNNB1, KRAS, TP53, CEBPA, CSF2, GATA3, PBX1, AKT1, CAV1, ERBB2, BAX, GNB1
 GO:0008283 15 / 263 6.4× 1.36e-8 2.23e-6 ✓ sig.
regulation of gene expression
CDKN2A, CTNNB1, CSF2, IL7, IRF1, MYB, NFKB1, FOXP1, ABL1, KMT2A, CDK4, CDK6
 GO:0010468 18 / 402 5.0× 2.00e-8 3.12e-6 ✓ sig.
positive regulation of gene expression
CDKN2A, CTNNB1, KRAS, TP53, CCL2, CEBPA, CEBPE, CSF2, GATA3, IL7, BCL11A, KMT2A
 GO:0010628 20 / 504 4.5× 2.35e-8 3.58e-6 ✓ sig.
cytokine-mediated signaling pathway
KRAS, CCL2, CEBPA, FLT3, IL7, STAT4, STAT6, TRAF3IP2, AKT1, CAV1, PTPRJ
 GO:0019221 11 / 145 8.5× 7.07e-8 9.03e-6 ✓ sig.
response to xenobiotic stimulus
CTNNB1, TP53, BAK1, GATA3, TRAF3IP2, ABL1, CDK4, NFE2L2, TIGAR, MDM2, CCND1, MMP2
 GO:0009410 13 / 248 5.9× 3.45e-7 3.42e-5 ✓ sig.
embryonic hemopoiesis
SH2B3, GATA3, PBX1, KMT2A, TAL1
 GO:0035162 5 / 18 31.3× 4.06e-7 3.93e-5 ✓ sig.
cellular response to tumor necrosis factor
CCL2, CD58, CEBPA, GATA3, NFKB1, FOXP1, AKT1, NFE2L2, NFKBIA
 GO:0071356 9 / 107 9.5× 4.72e-7 4.45e-5 ✓ sig.
myeloid cell differentiation
CDKN1C, CEBPA, CEBPE, CSF2, MYB, TAL1
 GO:0030099 6 / 35 19.3× 5.89e-7 5.37e-5 ✓ sig.
response to muscle stretch
NFKB1, TCAP, RYR2, NFKBIA, PIK3CA
 GO:0035994 5 / 20 28.1× 7.25e-7 6.40e-5 ✓ sig.
signal transduction
SH2B3, CELSR2, KRAS, ARHGAP31, CCL2, CCR6, CSF2, ELK3, ERG, GATA3, GRB10, HBS1L
 GO:0007165 41 / 2,125 2.2× 1.09e-6 8.91e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Endometrial hyperplasia Nasopharyngeal carcinoma 0.138 4 6.52e-10 6.35e-9 ✓ sig.
B-cell acute lymphoblastic leukemia Lymphoblastic leukemia 0.063 7 2.16e-9 1.99e-8 ✓ sig.
B-lymphoblastic leukemia/lymphoma Lymphoblastic leukemia 0.069 5 6.49e-9 5.74e-8 ✓ sig.
B-cell acute lymphoblastic leukemia B-lymphoblastic leukemia/lymphoma 0.067 5 8.45e-9 7.21e-8 ✓ sig.
Li-fraumeni syndrome Vulvar lichen sclerosus 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Endometrial hyperplasia Vulvar lichen sclerosus 0.182 2 3.80e-7 2.53e-6 ✓ sig.
B-lymphoblastic leukemia/lymphoma Carcinogenesis 0.086 3 1.28e-6 7.82e-6 ✓ sig.
B-lymphoblastic leukemia/lymphoma Vulvar lichen sclerosus 0.100 2 1.44e-6 8.70e-6 ✓ sig.
Carcinogenesis Nasopharyngeal carcinoma 0.079 3 2.04e-6 1.19e-5 ✓ sig.
Endometrial hyperplasia Li-fraumeni syndrome 0.143 2 3.79e-6 2.12e-5 ✓ sig.
B-lymphoblastic leukemia/lymphoma Li-fraumeni syndrome 0.087 2 1.44e-5 7.35e-5 ✓ sig.
Atypical multiple mole melanoma syndrome melanoma-pancreatic cancer syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
melanoma-pancreatic cancer syndrome Trisomy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Trisomy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Carcinogenesis Endometrial hyperplasia 0.074 2 5.78e-5 2.34e-4 ✓ sig.
melanoma-pancreatic cancer syndrome Vulvar lichen sclerosus 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Vulvar lichen sclerosus 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Trisomy Vulvar lichen sclerosus 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Brain stem neoplasms Intellectual developmental disorder growth other organ 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Brain stem neoplasms melanoma-pancreatic cancer syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Brain stem neoplasms Trisomy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Brain stem neoplasms 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Atypical multiple mole melanoma syndrome Li-fraumeni syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Li-fraumeni syndrome melanoma-pancreatic cancer syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Li-fraumeni syndrome Trisomy 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Carcinogenesis Gestational trophoblastic disease 0.053 1 1.17e-3 1.88e-3 ✓ sig.
B-lymphoblastic leukemia/lymphoma leukemia, acute myeloid, susceptibility to 0.050 1 1.23e-3 1.97e-3 ✓ sig.
B-cell acute lymphoblastic leukemia granulocytopenia with immunoglobulin abnormality 0.016 1 3.90e-3 4.94e-3 ✓ sig.