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 81

13 diseases · 26 shared-gene connections
13 Diseases
53 Unique genes
0.214 Avg. similarity score
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Most-connected disease (7 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 ⇵
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 7 7 1
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 7 7 1
Cecal neoplasms 6 6 4
Craniopharyngioma 6 6 2
Osteopathia striata with cranial sclerosis 6 6 2
Vascular calcification 6 6 2
Hepatoblastoma 4 4 4
Intestinal neoplasms 3 3 12
Wilms tumor 3 3 32
Bowen’s disease 1 1 4
Shukla-vernon syndrome 1 1 1
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 9 / 13 Cecal neoplasms, Craniopharyngioma, CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy, Hepatoblastoma and 5 more
AMER1 2 / 13 Osteopathia striata with cranial sclerosis, Wilms tumor
BCORL1 2 / 13 Shukla-vernon syndrome, Wilms tumor
CCND1 2 / 13 Bowen’s disease, Cecal neoplasms
IGF2 2 / 13 Hepatoblastoma, Wilms tumor
MGP 2 / 13 keutel syndrome, Vascular calcification
XPA 2 / 13 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, TP53
 KEGG 10 / 87 26.0× 3.54e-12 6.90e-10 ✓ sig.
Hepatocellular carcinoma
CCND1, CTNNB1, KRAS, BRAF, IGF2, TGFA, APC, BAX, CDKN1A, PRKCA, ARID1A, TP53
 KEGG 12 / 170 16.0× 7.06e-12 1.30e-9 ✓ sig.
Gastric cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, BCL2, CDKN1A, CDKN1B, MUC2, TP53
 KEGG 11 / 150 16.6× 3.88e-11 6.14e-9 ✓ sig.
Endometrial cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, CDKN1A, TP53
 KEGG 8 / 59 30.7× 1.55e-10 2.15e-8 ✓ sig.
Thyroid cancer
CCND1, CTNNB1, KRAS, BRAF, BAX, CDKN1A, TP53
 KEGG 7 / 37 42.9× 2.01e-10 2.71e-8 ✓ sig.
Prostate cancer
CCND1, CTNNB1, KRAS, BRAF, TGFA, BCL2, CDKN1A, CDKN1B, TP53
 KEGG 9 / 98 20.8× 3.64e-10 4.58e-8 ✓ sig.
Pathways in cancer
CCND1, CTNNB1, KRAS, BRAF, IGF2, TGFA, APC, BAX, BCL2, CDKN1A, CDKN1B, PRKCA
 KEGG 16 / 533 6.8× 5.86e-10 6.96e-8 ✓ sig.
Non-small cell lung cancer
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A, PRKCA, TP53
 KEGG 8 / 73 24.8× 8.95e-10 1.02e-7 ✓ sig.
Glioma
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A, PRKCA, TP53
 KEGG 8 / 76 23.9× 1.24e-9 1.35e-7 ✓ sig.
Pancreatic cancer
CCND1, KRAS, BRAF, TGFA, BAX, CDKN1A, BRCA2, TP53
 KEGG 8 / 77 23.5× 1.38e-9 1.48e-7 ✓ sig.
Endocrine resistance
CCND1, KRAS, BRAF, BAX, BCL2, CDKN1A, CDKN1B, TP53
 KEGG 8 / 99 18.3× 1.05e-8 9.06e-7 ✓ sig.
Breast cancer
CCND1, CTNNB1, KRAS, BRAF, APC, BAX, CDKN1A, BRCA2, TP53
 KEGG 9 / 148 13.8× 1.43e-8 1.19e-6 ✓ sig.
Proteoglycans in cancer
CCND1, CTNNB1, KRAS, BRAF, IGF2, CDKN1A, PRKCA, DROSHA, GPC3, TP53
 KEGG 10 / 204 11.1× 1.66e-8 1.35e-6 ✓ sig.
Chronic myeloid leukemia
CCND1, KRAS, BRAF, BAX, CDKN1A, CDKN1B, TP53
 KEGG 7 / 77 20.6× 4.10e-8 2.99e-6 ✓ sig.
Small cell lung cancer
CCND1, BAX, BCL2, CDKN1A, CDKN1B, MAX, TP53
 KEGG 7 / 93 17.1× 1.53e-7 9.48e-6 ✓ 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 ⇵
positive regulation of DNA-templated transcription
PPARGC1A, CTNNB1, NR1H4, ARID1A, BRCA2, MAX, MLLT1, MYCN, REST, SIX1, TP53, VHL
 GO:0045893 15 / 778 6.8× 2.44e-9 4.93e-7 ✓ sig.
cell population proliferation
CCND1, CTNNB1, KRAS, BAX, BCL2, BRCA2, MYCN, SIX2, TP53, PAX6
 GO:0008283 10 / 263 13.4× 2.94e-9 5.80e-7 ✓ sig.
kidney development
CTNNB1, BAX, BCL2, AMER1, GPC3, SIX1, SIX2, WT1
 GO:0001822 8 / 146 19.3× 7.54e-9 1.34e-6 ✓ sig.
negative regulation of transcription by RNA polymerase II
CCND1, CTNNB1, IGF2, PCNA, NR1H4, BCORL1, BCOR, DICER1, MAX, REST, SIX1, TP53
 GO:0000122 16 / 1,002 5.6× 9.43e-9 1.62e-6 ✓ sig.
negative regulation of neuron apoptotic process
CCND1, PPARGC1A, CTNNB1, KRAS, BRAF, BAX, BCL2, SIX1
 GO:0043524 8 / 160 17.6× 1.55e-8 2.50e-6 ✓ sig.
epithelial cell differentiation
CTNNB1, KRT20, PCNA, SIX1, SIX2, WT1, PAX6
 GO:0030855 7 / 110 22.4× 2.49e-8 3.76e-6 ✓ sig.
DNA damage response
CCND1, PCNA, APC, BAX, BCL2, CDKN1A, PRKCD, XPA, BRCA2, DGCR8, NONO, TP53
 GO:0006974 12 / 577 7.3× 5.63e-8 7.50e-6 ✓ sig.
branching involved in ureteric bud morphogenesis
CTNNB1, BCL2, GPC3, SIX1, WT1
 GO:0001658 5 / 45 39.2× 1.70e-7 1.88e-5 ✓ sig.
thymus development
CTNNB1, BRAF, BCL2, ASXL1, SIX1
 GO:0048538 5 / 50 35.3× 2.91e-7 2.97e-5 ✓ sig.
neuron apoptotic process
PPARGC1A, KRAS, BAX, BCL2, COL6A3, TP53
 GO:0051402 6 / 98 21.6× 3.35e-7 3.34e-5 ✓ sig.
negative regulation of cell population proliferation
CTNNB1, APC, BAX, BCL2, CDKN1A, CDKN1B, GPC3, TP53, VHL, WT1
 GO:0008285 10 / 444 7.9× 4.05e-7 3.92e-5 ✓ sig.
cellular senescence
CDKN1A, CDKN1B, PRKCD, BRCA2, TP53
 GO:0090398 5 / 57 30.9× 5.66e-7 5.20e-5 ✓ sig.
heart development
CTNNB1, PCNA, CDKN1A, CDKN1B, KCNQ1, BCOR, TP53, WT1
 GO:0007507 8 / 273 10.3× 9.39e-7 7.90e-5 ✓ sig.
response to gamma radiation
BAX, BCL2, BRCA2, TP53
 GO:0010332 4 / 27 52.2× 9.64e-7 8.07e-5 ✓ sig.
positive regulation of gene expression
PPARGC1A, CTNNB1, KRAS, BRAF, DROSHA, MYCN, REST, TP53, WT1, PAX6
 GO:0010628 10 / 504 7.0× 1.28e-6 1.01e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Osteopathia striata with cranial sclerosis Wilms tumor 0.061 2 4.18e-6 2.33e-5 ✓ sig.
Hepatoblastoma Wilms tumor 0.057 2 2.50e-5 1.24e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.49e-5 2.34e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
keutel syndrome Vascular calcification 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Vascular calcification 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Vascular calcification 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniopharyngioma CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Craniopharyngioma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Osteopathia striata with cranial sclerosis Vascular calcification 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Craniopharyngioma Vascular calcification 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Craniopharyngioma Osteopathia striata with cranial sclerosis 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Hepatoblastoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.40e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Hepatoblastoma 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cecal neoplasms CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cecal neoplasms Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Craniopharyngioma Hepatoblastoma 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cecal neoplasms Vascular calcification 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cecal neoplasms Osteopathia striata with cranial sclerosis 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Cecal neoplasms Craniopharyngioma 0.167 1 5.19e-4 1.04e-3 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Intestinal neoplasms 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Intestinal neoplasms 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Intestinal neoplasms xeroderma pigmentosum group A 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Bowen’s disease Cecal neoplasms 0.125 1 1.04e-3 1.72e-3 ✓ sig.
Shukla-vernon syndrome Wilms tumor 0.030 1 2.08e-3 2.95e-3 ✓ sig.