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 32

19 diseases · 71 shared-gene connections
19 Diseases
12 Unique genes
0.430 Avg. similarity score
Colorectal hamartoma Most-connected disease (16 links)
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Disease Searched: Gastric hamartomatous polyp 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 ⇵
Colorectal hamartoma 16 16 2
Fibrosarcoma 16 16 1
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 16 16 1
Neurodevelopmental disorder and/or vitreoretinopathy 16 16 1
Ovarian endometrioid adenocarcinoma with squamous differentiation 15 15 1
Cecal neoplasms 6 6 4
Vascular calcification 6 6 2
Calcifying nested epithelial stromal tumor of the liver 5 5 1
Ependymoblastoma 5 5 1
Lymph node palisaded myofibroblastoma 5 5 1
Malignant pericardial mesothelioma 5 5 2
Mental retardation, autosomal dominant 19 5 5 1
Neurodevelopmental disorder with spastic diplegia and visual defects 5 5 1
Osteopathia striata with cranial sclerosis 5 5 2
Pilomatrixoma 5 5 1
Uterine corpus atypical polypoid adenomyoma 5 5 2
Gastric hamartomatous polyp 4 4 2
Bowen’s disease 1 1 4
Keutel syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CTNNB1 17 / 19 Calcifying nested epithelial stromal tumor of the liver, Cecal neoplasms, Colorectal hamartoma, Ependymoblastoma and 13 more
CCND1 2 / 19 Bowen’s disease, Cecal neoplasms
KRAS 2 / 19 Cecal neoplasms, Uterine corpus atypical polypoid adenomyoma
MGP 2 / 19 Keutel syndrome, Vascular calcification
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 ⇵
Thyroid cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 37 108× 3.71e-8 2.35e-6 ✓ sig.
Apelin signaling pathway
CCND1, NRF1, PPARGC1A, TFAM, KRAS
 KEGG 5 / 140 35.7× 1.49e-7 7.92e-6 ✓ sig.
Endometrial cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 59 67.9× 2.52e-7 1.26e-5 ✓ sig.
Colorectal cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 87 46.0× 1.22e-6 4.94e-5 ✓ sig.
Human cytomegalovirus infection
CCND1, CTNNB1, KRAS, TP53, GNAS
 KEGG 5 / 226 22.1× 1.61e-6 6.28e-5 ✓ sig.
Prostate cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 98 40.9× 1.96e-6 7.44e-5 ✓ sig.
Endocrine resistance
CCND1, KRAS, TP53, GNAS
 KEGG 4 / 99 40.4× 2.04e-6 7.71e-5 ✓ sig.
Thyroid hormone signaling pathway
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 122 32.8× 4.71e-6 1.57e-4 ✓ sig.
Transcriptional Regulation by VENTX
CCND1, CTNNB1, TP53
 Reactome 3 / 38 79.0× 6.30e-6 1.99e-4 ✓ sig.
Bladder cancer
CCND1, KRAS, TP53
 KEGG 3 / 41 73.2× 7.95e-6 2.41e-4 ✓ sig.
Breast cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 148 27.0× 1.02e-5 2.95e-4 ✓ sig.
Gastric cancer
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 150 26.7× 1.07e-5 3.08e-4 ✓ sig.
Human papillomavirus infection
CCND1, CTNNB1, KRAS, TP53, GNAS
 KEGG 5 / 333 15.0× 1.07e-5 3.09e-4 ✓ sig.
Hepatitis C
CCND1, CTNNB1, KRAS, TP53
 KEGG 4 / 159 25.2× 1.35e-5 3.73e-4 ✓ sig.
Transcriptional activation of mitochondrial biogenesis
NRF1, PPARGC1A, TFAM
 Reactome 3 / 51 58.9× 1.54e-5 4.20e-4 ✓ 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
CCND1, CTNNB1, KRAS, TP53, BAP1
 GO:0008283 5 / 263 29.6× 3.88e-7 3.93e-5 ✓ sig.
negative regulation of neuron apoptotic process
CCND1, PPARGC1A, CTNNB1, KRAS
 GO:0043524 4 / 160 38.9× 2.43e-6 1.78e-4 ✓ sig.
hair follicle placode formation
CTNNB1, GNAS
 GO:0060789 2 / 5 623× 3.78e-6 2.53e-4 ✓ sig.
myoblast proliferation
CTNNB1, KRAS
 GO:0051450 2 / 12 260× 2.49e-5 1.09e-3 ✓ sig.
neuron apoptotic process
PPARGC1A, KRAS, TP53
 GO:0051402 3 / 98 47.7× 2.97e-5 1.24e-3 ✓ sig.
mitotic G1 DNA damage checkpoint signaling
CCND1, TP53
 GO:0031571 2 / 16 195× 4.51e-5 1.71e-3 ✓ sig.
negative regulation of epithelial cell differentiation
CCND1, KRAS
 GO:0030857 2 / 17 183× 5.11e-5 1.88e-3 ✓ sig.
glial cell proliferation
KRAS, TP53
 GO:0014009 2 / 18 173× 5.75e-5 2.05e-3 ✓ sig.
response to X-ray
CCND1, TP53
 GO:0010165 2 / 19 164× 6.43e-5 2.23e-3 ✓ sig.
positive regulation of cellular senescence
KRAS, TP53
 GO:2000774 2 / 20 156× 7.14e-5 2.40e-3 ✓ sig.
epithelial tube branching involved in lung morphogenesis
CTNNB1, KRAS
 GO:0060441 2 / 20 156× 7.14e-5 2.40e-3 ✓ sig.
tissue homeostasis
CTNNB1, BAP1
 GO:0001894 2 / 27 115× 1.32e-4 3.76e-3 ✓ sig.
positive regulation of gene expression
PPARGC1A, CTNNB1, KRAS, TP53
 GO:0010628 4 / 504 12.4× 2.18e-4 5.39e-3 ✓ sig.
T cell differentiation in thymus
CTNNB1, TP53
 GO:0033077 2 / 41 76.0× 3.06e-4 6.87e-3 ✓ sig.
embryonic organ development
CTNNB1, TP53
 GO:0048568 2 / 42 74.2× 3.21e-4 7.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Neurodevelopmental disorder and/or vitreoretinopathy Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Uterine corpus atypical polypoid adenomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Lymph node palisaded myofibroblastoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lymph node palisaded myofibroblastoma Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Lymph node palisaded myofibroblastoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Lymph node palisaded myofibroblastoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lymph node palisaded myofibroblastoma Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Mental retardation, autosomal dominant 19 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 19 Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Mental retardation, autosomal dominant 19 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Mental retardation, autosomal dominant 19 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 19 Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Calcifying nested epithelial stromal tumor of the liver Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder and/or vitreoretinopathy Uterine corpus atypical polypoid adenomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Neurodevelopmental disorder with spastic diplegia and visual defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder and/or vitreoretinopathy Neurodevelopmental disorder with spastic diplegia and visual defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Neurodevelopmental disorder with spastic diplegia and visual defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Neurodevelopmental disorder with spastic diplegia and visual defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder with spastic diplegia and visual defects Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ovarian endometrioid adenocarcinoma with squamous differentiation Uterine corpus atypical polypoid adenomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Pilomatrixoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder and/or vitreoretinopathy Pilomatrixoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Pilomatrixoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Pilomatrixoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ovarian endometrioid adenocarcinoma with squamous differentiation Pilomatrixoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Fibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Uterine corpus atypical polypoid adenomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ependymoblastoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ependymoblastoma Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ependymoblastoma Fibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Calcifying nested epithelial stromal tumor of the liver Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Calcifying nested epithelial stromal tumor of the liver Colorectal hamartoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Calcifying nested epithelial stromal tumor of the liver Fibrosarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Calcifying nested epithelial stromal tumor of the liver Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colorectal hamartoma Ependymoblastoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ependymoblastoma Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Neurodevelopmental disorder and/or vitreoretinopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Ovarian endometrioid adenocarcinoma with squamous differentiation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fibrosarcoma Uterine corpus atypical polypoid adenomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurodevelopmental disorder and/or vitreoretinopathy Osteopathia striata with cranial sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteopathia striata with cranial sclerosis Ovarian endometrioid adenocarcinoma with squamous differentiation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colorectal hamartoma Osteopathia striata with cranial sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibrosarcoma Osteopathia striata with cranial sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ovarian endometrioid adenocarcinoma with squamous differentiation Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodevelopmental disorder and/or vitreoretinopathy Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibrosarcoma Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colorectal hamartoma Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibrosarcoma Gastric hamartomatous polyp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Osteopathia striata with cranial sclerosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Malignant pericardial mesothelioma Ovarian endometrioid adenocarcinoma with squamous differentiation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colorectal hamartoma Malignant pericardial mesothelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Fibrosarcoma Malignant pericardial mesothelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Malignant pericardial mesothelioma Neurodevelopmental disorder and/or vitreoretinopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Malignant pericardial mesothelioma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Keutel syndrome Vascular calcification 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastric hamartomatous polyp Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gastric hamartomatous polyp Neurodevelopmental disorder and/or vitreoretinopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Colorectal hamartoma Gastric hamartomatous polyp 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cecal neoplasms Neurodevelopmental disorder and/or vitreoretinopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cecal neoplasms Fibrosarcoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cecal neoplasms Colorectal hamartoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cecal neoplasms Ovarian endometrioid adenocarcinoma with squamous differentiation 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cecal neoplasms Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Bowen’s disease Cecal neoplasms 0.143 1 7.75e-4 1.25e-3 ✓ sig.