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 124

11 diseases · 20 shared-gene connections
11 Diseases
65 Unique genes
0.274 Avg. similarity score
Keratoacanthoma Most-connected disease (8 links)
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Disease Searched: Keratoacanthoma 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 ⇵
Keratoacanthoma 8 8 9
Inverted urothelial papilloma 5 5 2
Lichen planus 5 5 4
Papilloma 5 5 15
Bladder papillary urothelial carcinoma 4 4 14
Epidermal nevus 3 3 9
Syringocystadenoma papilliferum 3 3 4
Dysplastic nevus 2 2 22
Infiltrating bladder urothelial carcinoma sarcomatoid variant 2 2 13
Malignant urinary system neoplasm 2 2 18
Bachmann-bupp syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HRAS 9 / 11 Bladder papillary urothelial carcinoma, Dysplastic nevus, Epidermal nevus, Inverted urothelial papilloma and 5 more
FGFR3 8 / 11 Bladder papillary urothelial carcinoma, Epidermal nevus, Infiltrating bladder urothelial carcinoma sarcomatoid variant, Inverted urothelial papilloma and 4 more
CDKN2A 6 / 11 Bladder papillary urothelial carcinoma, Dysplastic nevus, Infiltrating bladder urothelial carcinoma sarcomatoid variant, Keratoacanthoma and 2 more
TP53 6 / 11 Bladder papillary urothelial carcinoma, Dysplastic nevus, Infiltrating bladder urothelial carcinoma sarcomatoid variant, Keratoacanthoma and 2 more
KRAS 5 / 11 Epidermal nevus, Infiltrating bladder urothelial carcinoma sarcomatoid variant, Keratoacanthoma, Lichen planus and 1 more
PIK3CA 4 / 11 Epidermal nevus, Infiltrating bladder urothelial carcinoma sarcomatoid variant, Keratoacanthoma, Lichen planus
BRAF 3 / 11 Dysplastic nevus, Keratoacanthoma, Syringocystadenoma papilliferum
ERBB2 3 / 11 Bladder papillary urothelial carcinoma, Malignant urinary system neoplasm, Papilloma
NRAS 3 / 11 Dysplastic nevus, Epidermal nevus, Keratoacanthoma
ARID1A 2 / 11 Bladder papillary urothelial carcinoma, Malignant urinary system neoplasm
ATR 2 / 11 Dysplastic nevus, Malignant urinary system neoplasm
CDKN1A 2 / 11 Bladder papillary urothelial carcinoma, Papilloma
KDM6A 2 / 11 Bladder papillary urothelial carcinoma, Malignant urinary system neoplasm
ODC1 2 / 11 Bachmann-bupp syndrome, Papilloma
RB1 2 / 11 Bladder papillary urothelial carcinoma, Malignant urinary system neoplasm
SETD2 2 / 11 Dysplastic nevus, Malignant urinary system neoplasm
TSC1 2 / 11 Bladder papillary urothelial carcinoma, Infiltrating bladder urothelial carcinoma sarcomatoid variant
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 ⇵
Non-small cell lung cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFA, TP53, CDKN2A, AKT1
 KEGG 16 / 73 40.5× 3.09e-22 3.38e-19 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
FGFR3, HRAS, KRAS, NRAS, PIK3CA, EGFR, ERBB2, TGFA, FGFR2, AKT1, BRAF, NF1
 KEGG 15 / 80 34.6× 9.02e-20 6.48e-17 ✓ sig.
Hepatocellular carcinoma
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, NQO1, TGFA, TGFB1, TP53, CDKN2A
 KEGG 18 / 170 19.6× 5.85e-19 3.71e-16 ✓ sig.
Pathways in cancer
FGFR3, HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, NQO1, PTGS2, TGFA
 KEGG 26 / 533 9.0× 7.34e-19 4.58e-16 ✓ sig.
Bladder cancer
FGFR3, HRAS, KRAS, NRAS, CCND1, CDKN1A, EGFR, ERBB2, TP53, CDKN2A, RB1, BRAF
 KEGG 12 / 41 54.1× 1.51e-18 9.12e-16 ✓ sig.
Gastric cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFB1, TP53, FGFR2, AKT1
 KEGG 17 / 150 20.9× 1.94e-18 1.15e-15 ✓ sig.
Glioma
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, TGFA, TP53, CDKN2A, AKT1, RB1
 KEGG 14 / 76 34.0× 2.21e-18 1.27e-15 ✓ sig.
Prostate cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFA, TP53, FGFR2, AKT1
 KEGG 15 / 98 28.3× 2.31e-18 1.31e-15 ✓ sig.
Pancreatic cancer
KRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFA, TGFB1, TP53, CDKN2A, AKT1, RB1
 KEGG 14 / 77 33.6× 2.70e-18 1.52e-15 ✓ sig.
PI3K-Akt signaling pathway
FGFR3, HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFA, TP53, FGFR2
 KEGG 22 / 361 11.3× 6.49e-18 3.45e-15 ✓ sig.
Colorectal cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, TGFA, TGFB1, TP53, AKT1, RHOA
 KEGG 14 / 87 29.7× 1.67e-17 8.18e-15 ✓ sig.
Melanoma
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, TP53, CDKN2A, AKT1, RB1, BRAF
 KEGG 13 / 73 32.9× 6.44e-17 2.80e-14 ✓ sig.
Endocrine resistance
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TP53, CDKN2A, AKT1, RB1
 KEGG 14 / 99 26.1× 1.12e-16 4.67e-14 ✓ sig.
Endometrial cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TP53, AKT1, CTNNA1, BRAF
 KEGG 12 / 59 37.6× 1.99e-16 7.81e-14 ✓ sig.
Proteoglycans in cancer
HRAS, KRAS, NRAS, PIK3CA, CCND1, CDKN1A, EGFR, ERBB2, TGFB1, TP53, AKT1, RHOA
 KEGG 17 / 204 15.4× 3.81e-16 1.45e-13 ✓ 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 ⇵
cell population proliferation
FGFR3, KRAS, CCND1, EGFR, ERBB2, ODC1, TGFB1, TP53, AKT1, RB1, NF1, TSC1
 GO:0008283 14 / 263 15.3× 2.72e-13 1.44e-10 ✓ sig.
regulation of cell population proliferation
HRAS, EGFR, ERBB2, PTGS2, TGFB1, TP53, CTNNA1, BRAF, NF1, KIT, ERBB3, EZH2
 GO:0042127 12 / 201 17.2× 4.22e-12 1.75e-9 ✓ sig.
positive regulation of MAPK cascade
FGFR3, HRAS, EGFR, ERBB2, TGFA, TGFB1, FGFR2, KIT, ERBB4, ERBB3, TRAF7, HGF
 GO:0043410 12 / 224 15.4× 1.51e-11 5.53e-9 ✓ sig.
epidermal growth factor receptor signaling pathway
PIK3CA, EGFR, ERBB2, TGFA, AKT1, BRAF, ERBB4, ERBB3
 GO:0007173 8 / 64 35.9× 5.21e-11 1.70e-8 ✓ sig.
positive regulation of epithelial cell proliferation
HRAS, EGFR, ERBB2, TGFA, TGFB1, FGFR2, ERBB4, ERBB3
 GO:0050679 8 / 73 31.5× 1.54e-10 4.50e-8 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
FGFR3, PIK3CA, EGFR, TGFB1, HIP1, KIT, CSF1R, ERBB4, ERBB3, MTOR, HGF
 GO:0051897 11 / 217 14.6× 2.08e-10 5.88e-8 ✓ sig.
Ras protein signal transduction
HRAS, KRAS, NRAS, CDKN1A, TP53, CDKN2A, RB1, NF1
 GO:0007265 8 / 79 29.1× 2.95e-10 8.07e-8 ✓ sig.
positive regulation of cell population proliferation
FGFR3, HRAS, CCND1, CDKN1A, EGFR, ODC1, TGFA, TGFB1, FGFR2, KIT, CSF1R, ERBB4
 GO:0008284 15 / 532 8.1× 3.01e-10 8.19e-8 ✓ sig.
cell surface receptor protein tyrosine kinase signaling pathway
EGFR, ERBB2, ROS1, KIT, CSF1R, ERBB4, ERBB3, PTPRT, EPHA7
 GO:0007169 9 / 120 21.6× 3.24e-10 8.74e-8 ✓ sig.
apoptotic process
FGFR3, TGFB1, TP53, FGFR2, CDKN2A, AKT1, ERCC3, HIP1, ERCC2, CTNNA1, RB1, NF1
 GO:0006915 17 / 747 6.5× 4.39e-10 1.14e-7 ✓ sig.
regulation of ERK1 and ERK2 cascade
ERBB2, FGFR2, ROS1, NF1, TRAF7, EPHA7
 GO:0070372 6 / 33 52.3× 1.44e-9 3.20e-7 ✓ sig.
neuron apoptotic process
HRAS, KRAS, TGFB1, TP53, RB1, NF1, ERBB3, EPHA7
 GO:0051402 8 / 98 23.5× 1.69e-9 3.67e-7 ✓ sig.
negative regulation of apoptotic process
EGFR, ERBB2, PTGS2, SOD2, TP53, AKT1, CTNNA1, BRAF, CSF1R, ERBB4, ERBB3, MTOR
 GO:0043066 13 / 524 7.1× 2.47e-8 3.88e-6 ✓ sig.
phosphatidylinositol 3-kinase/protein kinase B signal transduction
PIK3CA, EGFR, ERBB2, AKT1, NF1, ERBB3, MTOR
 GO:0043491 7 / 92 21.9× 3.07e-8 4.69e-6 ✓ sig.
negative regulation of cell population proliferation
HRAS, CDKN1A, SOD2, TGFB1, TP53, CDKN2A, RB1, NF1, TSC1, CSF1R, ERBB4, RBM10
 GO:0008285 12 / 444 7.8× 3.60e-8 5.34e-6 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bladder papillary urothelial carcinoma Malignant urinary system neoplasm 0.240 6 1.10e-15 1.38e-14 ✓ sig.
Bladder papillary urothelial carcinoma Papilloma 0.217 5 3.46e-13 3.83e-12 ✓ sig.
Epidermal nevus Keratoacanthoma 0.300 3 5.65e-10 4.99e-9 ✓ sig.
Bladder papillary urothelial carcinoma Keratoacanthoma 0.188 3 4.62e-9 3.79e-8 ✓ sig.
Dysplastic nevus Malignant urinary system neoplasm 0.118 4 4.76e-9 3.90e-8 ✓ sig.
Keratoacanthoma Papilloma 0.176 3 5.87e-9 4.80e-8 ✓ sig.
Inverted urothelial papilloma Lichen planus 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Inverted urothelial papilloma Syringocystadenoma papilliferum 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Lichen planus Syringocystadenoma papilliferum 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Dysplastic nevus Keratoacanthoma 0.130 3 1.84e-8 1.42e-7 ✓ sig.
Bladder papillary urothelial carcinoma Infiltrating bladder urothelial carcinoma sarcomatoid variant 0.143 3 5.52e-8 3.99e-7 ✓ sig.
Inverted urothelial papilloma Keratoacanthoma 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Keratoacanthoma Lichen planus 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Keratoacanthoma Syringocystadenoma papilliferum 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Epidermal nevus Inverted urothelial papilloma 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Epidermal nevus Lichen planus 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Inverted urothelial papilloma Papilloma 0.133 2 7.59e-7 4.67e-6 ✓ sig.
Lichen planus Papilloma 0.133 2 7.59e-7 4.67e-6 ✓ sig.
Infiltrating bladder urothelial carcinoma sarcomatoid variant Keratoacanthoma 0.143 2 3.75e-6 2.12e-5 ✓ sig.
Bachmann-bupp syndrome Papilloma 0.067 1 9.04e-4 1.41e-3 ✓ sig.