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 121

10 diseases · 22 shared-gene connections
10 Diseases
21 Unique genes
0.240 Avg. similarity score
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Most-connected disease (7 links)
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Disease Searched: keutel syndrome 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 ⇵
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 7 7 1
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 7 7 1
Craniopharyngioma 6 6 2
Vascular calcification 6 6 2
Cecal neoplasms 5 5 4
Osteopathia striata with cranial sclerosis 5 5 2
Hepatoblastoma 3 3 4
Intestinal neoplasms 3 3 12
keutel syndrome 1 1 1
xeroderma pigmentosum group A 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CTNNB1 8 / 10 Cecal neoplasms, Craniopharyngioma, CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy, Hepatoblastoma and 4 more
MGP 2 / 10 keutel syndrome, Vascular calcification
XPA 2 / 10 Intestinal neoplasms, xeroderma pigmentosum group A
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 ⇵
Colorectal cancer
CCND1, CTNNB1, KRAS, BRAF, TGFA, APC, BAX, BCL2, CDKN1A
 KEGG 9 / 87 59.2× 9.84e-15 2.80e-12 ✓ sig.
Gastric cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, BCL2, CDKN1A, CDKN1B, MUC2
 KEGG 10 / 150 38.1× 2.14e-14 5.67e-12 ✓ sig.
Hepatocellular carcinoma
CCND1, CTNNB1, KRAS, BRAF, IGF2, TGFA, APC, BAX, CDKN1A, PRKCA
 KEGG 10 / 170 33.6× 7.63e-14 1.81e-11 ✓ sig.
Prostate cancer
CCND1, CTNNB1, KRAS, BRAF, TGFA, BCL2, CDKN1A, CDKN1B
 KEGG 8 / 98 46.7× 2.74e-12 5.04e-10 ✓ sig.
Endometrial cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, CDKN1A
 KEGG 7 / 59 67.9× 5.27e-12 9.33e-10 ✓ sig.
Pathways in cancer
CCND1, CTNNB1, KRAS, BRAF, IGF2, TGFA, APC, BAX, BCL2, CDKN1A, CDKN1B, PRKCA
 KEGG 12 / 533 12.9× 1.05e-11 1.77e-9 ✓ sig.
Non-small cell lung cancer
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A, PRKCA
 KEGG 7 / 73 54.8× 2.48e-11 3.80e-9 ✓ sig.
Thyroid cancer
CCND1, CTNNB1, KRAS, BRAF, BAX, CDKN1A
 KEGG 6 / 37 92.7× 2.93e-11 4.46e-9 ✓ sig.
Glioma
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A, PRKCA
 KEGG 7 / 76 52.7× 3.32e-11 4.97e-9 ✓ sig.
Endocrine resistance
CCND1, KRAS, BRAF, BAX, BCL2, CDKN1A, CDKN1B
 KEGG 7 / 99 40.4× 2.21e-10 2.77e-8 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
CCND1, KRAS, BAX, BCL2, CDKN1B, PRKCA, PRKCD
 KEGG 7 / 101 39.6× 2.54e-10 3.12e-8 ✓ sig.
Pancreatic cancer
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A
 KEGG 6 / 77 44.6× 2.86e-9 2.73e-7 ✓ sig.
Chronic myeloid leukemia
CCND1, KRAS, BRAF, BAX, CDKN1A, CDKN1B
 KEGG 6 / 77 44.6× 2.86e-9 2.73e-7 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
KRAS, BRAF, TGFA, BAX, BCL2, PRKCA
 KEGG 6 / 80 42.9× 3.62e-9 3.38e-7 ✓ sig.
Breast cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, CDKN1A
 KEGG 7 / 148 27.0× 3.77e-9 3.51e-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 ⇵
negative regulation of neuron apoptotic process
CCND1, CTNNB1, KRAS, BRAF, BAX, BCL2
 GO:0043524 6 / 160 33.4× 1.75e-8 2.75e-6 ✓ sig.
DNA damage response
CCND1, PCNA, APC, BAX, BCL2, CDKN1A, PRKCD, XPA
 GO:0006974 8 / 577 12.3× 1.12e-7 1.32e-5 ✓ sig.
positive regulation of cell population proliferation
CCND1, CTNNB1, IGF2, TGFA, BCL2, CDKN1A, CDKN1B
 GO:0008284 7 / 532 11.7× 1.20e-6 9.64e-5 ✓ sig.
regulation of nitrogen utilization
BAX, BCL2
 GO:0006808 2 / 2 890× 1.20e-6 9.65e-5 ✓ sig.
positive regulation of developmental pigmentation
BAX, BCL2
 GO:0048087 2 / 2 890× 1.20e-6 9.65e-5 ✓ sig.
negative regulation of cardiac muscle tissue regeneration
CDKN1A, CDKN1B
 GO:1905179 2 / 2 890× 1.20e-6 9.65e-5 ✓ sig.
epithelial cell apoptotic process
BAX, BCL2, CDKN1B
 GO:1904019 3 / 20 133× 1.38e-6 1.08e-4 ✓ sig.
response to toxic substance
BAX, BCL2, PRKCA, XPA
 GO:0009636 4 / 83 42.9× 2.04e-6 1.48e-4 ✓ sig.
response to estradiol
CCND1, CTNNB1, PCNA, PRKCA
 GO:0032355 4 / 84 42.4× 2.14e-6 1.53e-4 ✓ sig.
G1/S transition of mitotic cell cycle
CCND1, BCL2, CDKN1A, CDKN1B
 GO:0000082 4 / 85 41.9× 2.25e-6 1.60e-4 ✓ sig.
retinal cell programmed cell death
BAX, BCL2
 GO:0046666 2 / 3 593× 3.61e-6 2.33e-4 ✓ sig.
negative regulation of cyclin-dependent protein kinase activity
CDKN1A, CDKN1B
 GO:1904030 2 / 3 593× 3.61e-6 2.33e-4 ✓ sig.
positive regulation of DNA replication
PCNA, CDKN1A, CDKN1B
 GO:0045740 3 / 29 92.1× 4.39e-6 2.72e-4 ✓ sig.
negative regulation of cell population proliferation
CTNNB1, APC, BAX, BCL2, CDKN1A, CDKN1B
 GO:0008285 6 / 444 12.0× 6.97e-6 3.95e-4 ✓ sig.
protein kinase C signaling
PRKCA, PRKCD
 GO:0070528 2 / 4 445× 7.21e-6 4.06e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.49e-5 2.33e-4 ✓ sig.
keutel syndrome Vascular calcification 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Craniopharyngioma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Craniopharyngioma CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.333 1 1.30e-4 3.93e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Vascular calcification 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Vascular calcification 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Craniopharyngioma Vascular calcification 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Osteopathia striata with cranial sclerosis Vascular calcification 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Craniopharyngioma Osteopathia striata with cranial sclerosis 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Cecal neoplasms CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Hepatoblastoma 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Hepatoblastoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cecal neoplasms Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Craniopharyngioma Hepatoblastoma 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Cecal neoplasms Vascular calcification 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Cecal neoplasms Osteopathia striata with cranial sclerosis 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Cecal neoplasms Craniopharyngioma 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Intestinal neoplasms 0.077 1 7.79e-4 1.40e-3 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Intestinal neoplasms 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Intestinal neoplasms xeroderma pigmentosum group A 0.077 1 7.79e-4 1.40e-3 ✓ sig.