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 17

26 diseases · 82 shared-gene connections
26 Diseases
29 Unique genes
0.407 Avg. similarity score
Brain tumor-polyposis syndrome Most-connected disease (18 links)
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Disease Searched: Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) 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 ⇵
Brain tumor-polyposis syndrome 18 18 1
Gastric adenocarcinoma and proximal polyposis of the stomach 18 18 1
Appendix villous adenoma 16 16 3
Colon juvenile polyp 15 15 1
Epidermal inclusion cyst 14 14 1
Cenani-lenz syndrome 7 7 2
Gastrointestinal neoplasms 7 7 4
Adenoma of small intestine 5 5 2
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) 5 5 1
Colon neuroendocrine tumor g1 5 5 2
Colorectal sessile serrated adenoma/polyp 5 5 3
Desmoid disease, hereditary 5 5 1
Duodenal villous adenoma 5 5 2
Gardner syndrome 5 5 1
Juvenile nasopharyngeal angiofibroma 5 5 1
Pyloric gland adenoma 5 5 4
Intestinal polyps 4 4 6
Tumor of duodenum 4 4 3
Gastrointestinal hemorrhage 3 3 6
Rectal villous adenoma 3 3 7
Sclerosteosis 3 3 2
Chronic pancreatitis 2 2 8
Congenital myasthenic syndrome 17 2 2 1
Bone dysplasia with increased bone density 1 1 1
Hyperemesis gravidarum 1 1 4
Visceral neuropathy, familial, 2, autosomal recessive 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APC 20 / 26 Adenoma of small intestine, Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc), Appendix villous adenoma, Brain tumor-polyposis syndrome and 16 more
KRAS 8 / 26 Adenoma of small intestine, Appendix villous adenoma, Chronic pancreatitis, Colon neuroendocrine tumor g1 and 4 more
BRAF 4 / 26 Chronic pancreatitis, Colorectal sessile serrated adenoma/polyp, Rectal villous adenoma, Tumor of duodenum
GNAS 4 / 26 Chronic pancreatitis, Pyloric gland adenoma, Rectal villous adenoma, Tumor of duodenum
LRP4 3 / 26 Cenani-lenz syndrome, Congenital myasthenic syndrome 17, Sclerosteosis
SMAD4 3 / 26 Chronic pancreatitis, Pyloric gland adenoma, Rectal villous adenoma
ERBB2 2 / 26 Gastrointestinal neoplasms, Visceral neuropathy, familial, 2, autosomal recessive
GDF15 2 / 26 Gastrointestinal neoplasms, Hyperemesis gravidarum
SOST 2 / 26 Bone dysplasia with increased bone density, Sclerosteosis
TP53 2 / 26 Appendix villous adenoma, Rectal villous adenoma
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 ⇵
Endocrine resistance
ERBB2, CCND1, JUN, BRAF, KRAS, GNAS, TP53, CDKN2A
 KEGG 8 / 99 33.5× 5.95e-11 7.41e-9 ✓ sig.
Pancreatic cancer
ERBB2, CCND1, BRAF, KRAS, SMAD4, TP53, CDKN2A
 KEGG 7 / 77 37.6× 4.70e-10 4.71e-8 ✓ sig.
Bladder cancer
ERBB2, CCND1, BRAF, KRAS, TP53, CDKN2A
 KEGG 6 / 41 60.6× 4.84e-10 4.85e-8 ✓ sig.
Colorectal cancer
APC, CCND1, JUN, BRAF, KRAS, SMAD4, TP53
 KEGG 7 / 87 33.3× 1.12e-9 1.03e-7 ✓ sig.
Endometrial cancer
APC, ERBB2, CCND1, BRAF, KRAS, TP53
 KEGG 6 / 59 42.1× 4.71e-9 3.76e-7 ✓ sig.
Non-small cell lung cancer
ERBB2, CCND1, BRAF, KRAS, TP53, CDKN2A
 KEGG 6 / 73 34.0× 1.74e-8 1.21e-6 ✓ sig.
Pathways in cancer
APC, ERBB2, CCND1, JUN, PTGS2, BRAF, KRAS, SMAD4, GNAS, TP53, CDKN2A
 KEGG 11 / 533 8.5× 1.98e-8 1.36e-6 ✓ sig.
Chronic myeloid leukemia
CCND1, BRAF, KRAS, SMAD4, TP53, CDKN2A
 KEGG 6 / 77 32.3× 2.41e-8 1.61e-6 ✓ sig.
Breast cancer
APC, ERBB2, CCND1, JUN, BRAF, KRAS, TP53
 KEGG 7 / 148 19.6× 4.66e-8 2.86e-6 ✓ sig.
Gastric cancer
APC, ERBB2, CCND1, BRAF, KRAS, SMAD4, TP53
 KEGG 7 / 150 19.3× 5.11e-8 3.10e-6 ✓ sig.
Hepatocellular carcinoma
APC, CCND1, BRAF, KRAS, SMAD4, TP53, CDKN2A
 KEGG 7 / 170 17.1× 1.21e-7 6.61e-6 ✓ sig.
Melanoma
CCND1, BRAF, KRAS, TP53, CDKN2A
 KEGG 5 / 73 28.4× 7.65e-7 3.30e-5 ✓ sig.
Human T-cell leukemia virus 1 infection
CSF2, CCND1, JUN, KRAS, SMAD4, TP53, CDKN2A
 KEGG 7 / 224 12.9× 7.87e-7 3.38e-5 ✓ sig.
Glioma
CCND1, BRAF, KRAS, TP53, CDKN2A
 KEGG 5 / 76 27.2× 9.37e-7 3.95e-5 ✓ sig.
Thyroid cancer
CCND1, BRAF, KRAS, TP53
 KEGG 4 / 37 44.8× 1.71e-6 6.65e-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 ⇵
regulation of cell population proliferation
BCL6, CSF2, ERBB2, JUN, PTGS1, PTGS2, BRAF, SMAD4, TP53
 GO:0042127 9 / 201 28.9× 1.34e-11 5.00e-9 ✓ sig.
cell population proliferation
BCL6, CSF2, ERBB2, CCND1, JUN, KRAS, SMAD4, TP53
 GO:0008283 8 / 263 19.6× 4.60e-9 8.89e-7 ✓ sig.
negative regulation of apoptotic process
AVP, BCL6, LTF, ERBB2, GNRH1, JUN, PTGS2, BRAF, TP53
 GO:0043066 9 / 524 11.1× 6.08e-8 8.37e-6 ✓ sig.
positive regulation of gene expression
AVP, CSF2, ERBB2, BRAF, KRAS, SMAD4, TP53, CDKN2A
 GO:0010628 8 / 504 10.2× 6.90e-7 6.35e-5 ✓ sig.
cyclooxygenase pathway
PTGS1, PTGS2
 GO:0019371 2 / 3 430× 6.97e-6 4.11e-4 ✓ sig.
response to steroid hormone
CCND1, GNRH1, JUN
 GO:0048545 3 / 30 64.4× 1.33e-5 6.77e-4 ✓ sig.
negative regulation of osteoclast development
LTF, FBXW7
 GO:2001205 2 / 5 258× 2.32e-5 1.03e-3 ✓ sig.
transforming growth factor beta receptor signaling pathway
GDF15, JUN, SMAD4, TP53
 GO:0007179 4 / 112 23.0× 2.59e-5 1.12e-3 ✓ sig.
Wnt signaling pathway
APC, LRP4, HIC1, CCND1, SOST
 GO:0016055 5 / 232 13.9× 2.63e-5 1.13e-3 ✓ sig.
negative regulation of cell growth
BCL6, SMAD4, TP53, CDKN2A
 GO:0030308 4 / 115 22.4× 2.87e-5 1.21e-3 ✓ sig.
negative regulation of immature T cell proliferation in thymus
ERBB2, CDKN2A
 GO:0033088 2 / 6 215× 3.47e-5 1.40e-3 ✓ sig.
negative regulation of canonical Wnt signaling pathway
APC, LRP4, SOST, SMAD4
 GO:0090090 4 / 150 17.2× 8.10e-5 2.65e-3 ✓ sig.
response to salt stress
AVP, TP53
 GO:0009651 2 / 9 143× 8.32e-5 2.70e-3 ✓ sig.
negative regulation of cyclin-dependent protein serine/threonine kinase activity
APC, CDKN2A
 GO:0045736 2 / 9 143× 8.32e-5 2.70e-3 ✓ sig.
positive regulation of prostaglandin biosynthetic process
AVP, PTGS2
 GO:0031394 2 / 9 143× 8.32e-5 2.70e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pyloric gland adenoma Rectal villous adenoma 0.600 3 6.46e-12 6.55e-11 ✓ sig.
Pyloric gland adenoma Tumor of duodenum 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Rectal villous adenoma Tumor of duodenum 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Chronic pancreatitis Pyloric gland adenoma 0.250 2 3.75e-7 2.42e-6 ✓ sig.
Chronic pancreatitis Rectal villous adenoma 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Duodenal villous adenoma Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Colorectal sessile serrated adenoma/polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Duodenal villous adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Desmoid disease, hereditary Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Desmoid disease, hereditary 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Desmoid disease, hereditary 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Desmoid disease, hereditary Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Desmoid disease, hereditary 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal sessile serrated adenoma/polyp Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Colorectal sessile serrated adenoma/polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Colorectal sessile serrated adenoma/polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal sessile serrated adenoma/polyp Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenoma of small intestine Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Duodenal villous adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Duodenal villous adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Duodenal villous adenoma Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epidermal inclusion cyst Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Gardner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gardner syndrome Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Gardner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Gardner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epidermal inclusion cyst Gardner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Juvenile nasopharyngeal angiofibroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Juvenile nasopharyngeal angiofibroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Juvenile nasopharyngeal angiofibroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Juvenile nasopharyngeal angiofibroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epidermal inclusion cyst Juvenile nasopharyngeal angiofibroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) Colon juvenile polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) Appendix villous adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) Brain tumor-polyposis syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenoma of small intestine Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenoma of small intestine Colon juvenile polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenoma of small intestine Appendix villous adenoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenoma of small intestine Brain tumor-polyposis syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon neuroendocrine tumor g1 Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomatous polyposis coli (thyroid papillary carcinoma in patients with apc) Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Brain tumor-polyposis syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Colon juvenile polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Colon neuroendocrine tumor g1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Appendix villous adenoma Colon neuroendocrine tumor g1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon neuroendocrine tumor g1 Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Colon neuroendocrine tumor g1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Epidermal inclusion cyst 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon juvenile polyp Gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain tumor-polyposis syndrome Colon juvenile polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cenani-lenz syndrome Colon juvenile polyp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cenani-lenz syndrome Epidermal inclusion cyst 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Tumor of duodenum 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain tumor-polyposis syndrome Tumor of duodenum 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Appendix villous adenoma Cenani-lenz syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cenani-lenz syndrome Gastric adenocarcinoma and proximal polyposis of the stomach 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital myasthenic syndrome 17 Sclerosteosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cenani-lenz syndrome Congenital myasthenic syndrome 17 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain tumor-polyposis syndrome Cenani-lenz syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Bone dysplasia with increased bone density Sclerosteosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Pyloric gland adenoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Brain tumor-polyposis syndrome Pyloric gland adenoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cenani-lenz syndrome Sclerosteosis 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Gastrointestinal neoplasms Visceral neuropathy, familial, 2, autosomal recessive 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Epidermal inclusion cyst Gastrointestinal neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Colon juvenile polyp Gastrointestinal neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Appendix villous adenoma Gastrointestinal neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal neoplasms 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Colon juvenile polyp Intestinal polyps 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Appendix villous adenoma Intestinal polyps 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Intestinal polyps 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Brain tumor-polyposis syndrome Intestinal polyps 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Appendix villous adenoma Gastrointestinal hemorrhage 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal hemorrhage 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal hemorrhage 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Gastrointestinal neoplasms Hyperemesis gravidarum 0.125 1 1.03e-3 1.57e-3 ✓ sig.