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 214

8 diseases · 8 shared-gene connections
8 Diseases
148 Unique genes
0.033 Avg. similarity score
Kidney neoplasms Most-connected disease (4 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 ⇵
Kidney neoplasms 4 4 40
Sezary syndrome 4 4 27
Cervicitis 2 2 1
Small cell lung carcinoma 2 2 91
Borderline personality disorder 1 1 1
Nasopalpebral lipoma-coloboma syndrome 1 1 1
immunodeficiency 109 with lymphoproliferation 1 1 1
snijders blok-campeau syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
IL32 3 / 8 Cervicitis, Kidney neoplasms, Sezary syndrome
BRAF 2 / 8 Kidney neoplasms, Sezary syndrome
CDKN1B 2 / 8 Kidney neoplasms, Sezary syndrome
CHD3 2 / 8 Sezary syndrome, snijders blok-campeau syndrome
CREBBP 2 / 8 Sezary syndrome, Small cell lung carcinoma
MAPK1 2 / 8 Kidney neoplasms, Sezary syndrome
NDRG1 2 / 8 Kidney neoplasms, Small cell lung carcinoma
PTEN 2 / 8 Sezary syndrome, Small cell lung carcinoma
RB1 2 / 8 Sezary syndrome, Small cell lung carcinoma
SMARCA4 2 / 8 Sezary syndrome, Small cell lung carcinoma
TNFRSF9 2 / 8 immunodeficiency 109 with lymphoproliferation, Kidney neoplasms
TP53 2 / 8 Sezary syndrome, Small cell lung carcinoma
TPH1 2 / 8 Borderline personality disorder, Kidney neoplasms
ZDBF2 2 / 8 Nasopalpebral lipoma-coloboma syndrome, Small cell lung 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 ⇵
Prostate cancer
BRAF, CCND1, CDKN1B, MAPK1, MAPK3, RAF1, CREBBP, PTEN, RB1, TP53, ZEB1, EGFR
 KEGG 14 / 98 11.6× 1.34e-11 2.34e-9 ✓ sig.
Melanoma
BRAF, CCND1, MAPK1, MAPK3, RAF1, CDKN2A, PTEN, RB1, TP53, EGFR, FGFR1
 KEGG 11 / 73 12.2× 1.27e-9 1.37e-7 ✓ sig.
Non-small cell lung cancer
BRAF, CCND1, MAPK1, MAPK3, RAF1, RASSF5, CDKN2A, PLCG1, RB1, TP53, EGFR
 KEGG 11 / 73 12.2× 1.27e-9 1.37e-7 ✓ sig.
Bladder cancer
BRAF, CCND1, MAPK1, MAPK3, RAF1, CDKN2A, RB1, TP53, EGFR
 KEGG 9 / 41 17.8× 1.29e-9 1.39e-7 ✓ sig.
Pathways in cancer
BRAF, CCND1, CDKN1B, GSTT1, IL2, MAPK1, MAPK3, PTGS2, RAF1, RASSF5, VHL, CDKN2A
 KEGG 26 / 533 4.0× 1.48e-9 1.58e-7 ✓ sig.
Glioma
BRAF, CCND1, MAPK1, MAPK3, RAF1, CDKN2A, PLCG1, PTEN, RB1, TP53, EGFR
 KEGG 11 / 76 11.7× 1.97e-9 2.03e-7 ✓ sig.
Human T-cell leukemia virus 1 infection
CCND1, IL2, MAPK1, MAPK3, RANBP1, CDKN2A, CREBBP, IL2RG, PTEN, RB1, TP53, ADCY1
 KEGG 17 / 224 6.2× 2.13e-9 2.17e-7 ✓ sig.
Hepatocellular carcinoma
BRAF, CCND1, GSTT1, MAPK1, MAPK3, RAF1, ARID1A, CDKN2A, PLCG1, PTEN, RB1, SMARCA4
 KEGG 14 / 170 6.7× 2.15e-8 1.71e-6 ✓ sig.
Pancreatic cancer
BRAF, CCND1, MAPK1, MAPK3, RAF1, CDKN2A, RB1, TP53, BRCA2, EGFR
 KEGG 10 / 77 10.5× 3.22e-8 2.44e-6 ✓ sig.
Endocrine resistance
BRAF, CCND1, CDKN1B, MAPK1, MAPK3, RAF1, CDKN2A, RB1, TP53, ADCY1, EGFR
 KEGG 11 / 99 9.0× 3.41e-8 2.55e-6 ✓ sig.
FoxO signaling pathway
BRAF, CCND1, CDKN1B, MAPK1, MAPK3, RAF1, SOD2, TNFSF10, CREBBP, PTEN, EGFR, EP300
 KEGG 12 / 133 7.3× 8.37e-8 5.61e-6 ✓ sig.
Breast cancer
BRAF, CCND1, MAPK1, MAPK3, RAF1, PTEN, RB1, TP53, BRCA2, EGFR, FGFR1, KIT
 KEGG 12 / 148 6.6× 2.72e-7 1.57e-5 ✓ sig.
Negative feedback regulation of MAPK pathway
BRAF, MAPK1, MAPK3, RAF1
 Reactome 4 / 6 54.1× 3.26e-7 1.84e-5 ✓ sig.
Chronic myeloid leukemia
BRAF, CCND1, CDKN1B, MAPK1, MAPK3, RAF1, CDKN2A, RB1, TP53
 KEGG 9 / 77 9.5× 4.06e-7 2.23e-5 ✓ sig.
Cellular senescence
CCND1, EIF4EBP1, MAPK1, MAPK3, RAF1, RASSF5, TSC2, CDKN2A, PTEN, RB1, TP53, HLA-B
 KEGG 12 / 157 6.2× 5.16e-7 2.75e-5 ✓ 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 population proliferation
BAP1, CDKN1B, NDRG1, RAF1, SOD2, TNFRSF9, TSC2, VHL, CDKN2A, PTEN, RB1, TP53
 GO:0008285 18 / 444 5.1× 1.50e-8 2.43e-6 ✓ sig.
heart development
BCOR, CDKN1B, MAPK1, SOD2, TSC2, PRKG1, PTEN, TP53, ASCL1, BMP6, DYNC2H1, EP300
 GO:0007507 14 / 273 6.5× 3.71e-8 5.27e-6 ✓ sig.
chromatin organization
BAP1, BCOR, HLTF, ARID1A, BRD9, CHD3, DNMT3A, KMT2C, KMT2D, RB1, SMARCA4, TET2
 GO:0006325 17 / 449 4.8× 1.04e-7 1.24e-5 ✓ sig.
positive regulation of cell differentiation
VHL, ARID1A, RPS6KA1, SMARCA4, TP73, FGFR1, INSM1, SOX2
 GO:0045597 8 / 83 12.2× 3.06e-7 3.10e-5 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
CCND1, CDKN1B, ARID1A, CDKN2A, RB1, SMARCA4, ID2
 GO:2000045 7 / 57 15.5× 3.22e-7 3.22e-5 ✓ sig.
face development
BRAF, MAPK1, MAPK3, RAF1, ALDH1A2
 GO:0060324 5 / 22 28.7× 6.88e-7 6.12e-5 ✓ sig.
regulation of gene expression
BAP1, MAPK3, VHL, CDKN2A, DNMT3A, IL2RG, TET2, TP73, ASCL1, FGFR1, ID2, INSM1
 GO:0010468 15 / 402 4.7× 7.34e-7 6.46e-5 ✓ sig.
positive regulation of transcription by RNA polymerase II
HLTF, IL2, MAPK3, RAF1, CD28, CDKN2A, CREBBP, KMT2C, KMT2D, PTEN, RB1, RPS6KA1
 GO:0045944 27 / 1,208 2.8× 8.48e-7 7.25e-5 ✓ sig.
negative regulation of apoptotic process
AURKA, AXL, BRAF, FIGNL1, IL2, PTGS2, RAF1, SOD2, TPT1, VHL, CD28, RPS6KA1
 GO:0043066 17 / 524 4.1× 9.04e-7 7.63e-5 ✓ sig.
cell population proliferation
BAP1, CCND1, RB1, TP53, ZEB1, ALDH1A2, BRCA2, CNTNAP2, EGFR, FGFR1, INSM1, KIT
 GO:0008283 12 / 263 5.8× 1.26e-6 9.98e-5 ✓ sig.
neuron differentiation
CCND1, DNMT3A, RB1, ALDH1A2, ASCL1, BMP6, DYNC2H1, EGFR, ID2, INSM1, SOX2
 GO:0030182 11 / 222 6.3× 1.60e-6 1.20e-4 ✓ sig.
chromatin remodeling
AURKA, BCOR, ARID1A, BRD9, CHD3, CREBBP, KMT2C, RB1, SMARCA4, BRCA2, EP300, PHC1
 GO:0006338 13 / 320 5.1× 1.64e-6 1.23e-4 ✓ sig.
mammary gland epithelial cell proliferation
CCND1, MAPK1, CDKN2A, ID2
 GO:0033598 4 / 12 42.1× 1.78e-6 1.31e-4 ✓ sig.
apoptotic process
AURKA, AXL, CDKN1B, MAPK1, MAPK3, RAF1, RASSF5, TNFRSF9, TNFSF10, TNFRSF1B, CDKN2A, PTEN
 GO:0006915 20 / 747 3.4× 1.86e-6 1.36e-4 ✓ sig.
response to epidermal growth factor
MAPK1, MAPK3, ASCL1
 GO:0070849 3 / 5 75.8× 4.81e-6 2.91e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Sezary syndrome Small cell lung carcinoma 0.044 5 4.70e-7 3.10e-6 ✓ sig.
Kidney neoplasms Sezary syndrome 0.063 4 6.56e-7 4.21e-6 ✓ sig.
Cervicitis Sezary syndrome 0.036 1 1.75e-3 2.59e-3 ✓ sig.
Sezary syndrome snijders blok-campeau syndrome 0.036 1 1.75e-3 2.59e-3 ✓ sig.
Borderline personality disorder Kidney neoplasms 0.024 1 2.60e-3 3.50e-3 ✓ sig.
Cervicitis Kidney neoplasms 0.024 1 2.60e-3 3.50e-3 ✓ sig.
immunodeficiency 109 with lymphoproliferation Kidney neoplasms 0.024 1 2.60e-3 3.50e-3 ✓ sig.
Nasopalpebral lipoma-coloboma syndrome Small cell lung carcinoma 0.011 1 5.91e-3 7.13e-3 ✓ sig.