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 9

31 diseases · 53 shared-gene connections
31 Diseases
270 Unique genes
0.199 Avg. similarity score
Cecal neoplasms Most-connected disease (9 links)
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Disease Searched: Small cell lung carcinoma 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 ⇵
Cecal neoplasms 9 9 4
Craniopharyngioma 9 9 2
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 7 7 1
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 7 7 1
Osteopathia striata with cranial sclerosis 6 6 2
Sezary syndrome 6 6 27
Vascular calcification 6 6 2
Weyers acrofacial dysostosis 6 6 3
Hemangiosarcoma 5 5 18
Acrofacial dysostosis 4 4 4
Ellis-van creveld syndrome 4 4 9
Endometrial hyperplasia 4 4 10
Hepatoblastoma 4 4 4
Curry-hall syndrome 3 3 2
Tethered cord syndrome 3 3 2
Wilms tumor 3 3 32
Hairy cell leukemia 2 2 1
Nasopharyngeal carcinoma 2 2 22
Small cell lung carcinoma 2 2 91
Uterine neoplasms 2 2 38
immune dysregulation, autoimmunity, and autoinflammation 2 2 1
Bowen’s disease 1 1 4
Cervicitis 1 1 1
Craniofaciocardiohepatic syndrome 1 1 1
Nasopalpebral lipoma-coloboma syndrome 1 1 1
Osteosarcoma 1 1 57
SF3B4-related acrofacial dysostosis 1 1 1
Shukla-vernon syndrome 1 1 1
keutel syndrome 1 1 1
primary ciliary dyskinesia 14 1 1 1
snijders blok-campeau syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CTNNB1 12 / 31 Cecal neoplasms, Craniopharyngioma, CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy, Endometrial hyperplasia and 8 more
TP53 7 / 31 Endometrial hyperplasia, Hemangiosarcoma, Nasopharyngeal carcinoma, Osteosarcoma and 3 more
CCND1 5 / 31 Bowen’s disease, Cecal neoplasms, Hemangiosarcoma, Nasopharyngeal carcinoma and 1 more
KRAS 5 / 31 Cecal neoplasms, Endometrial hyperplasia, Hemangiosarcoma, Nasopharyngeal carcinoma and 1 more
BRAF 4 / 31 Craniopharyngioma, Hairy cell leukemia, Sezary syndrome, Tethered cord syndrome
EVC 4 / 31 Acrofacial dysostosis, Curry-hall syndrome, Ellis-van creveld syndrome, Weyers acrofacial dysostosis
EVC2 4 / 31 Acrofacial dysostosis, Curry-hall syndrome, Ellis-van creveld syndrome, Weyers acrofacial dysostosis
PTEN 4 / 31 Endometrial hyperplasia, Nasopharyngeal carcinoma, Sezary syndrome, Small cell lung carcinoma
ARID1A 3 / 31 Nasopharyngeal carcinoma, Sezary syndrome, Wilms tumor
CDKN2A 3 / 31 Endometrial hyperplasia, Nasopharyngeal carcinoma, Sezary syndrome
CSF3 3 / 31 Hemangiosarcoma, Small cell lung carcinoma, Uterine neoplasms
EGFR 3 / 31 Osteosarcoma, Small cell lung carcinoma, Uterine neoplasms
MYC 3 / 31 Hemangiosarcoma, Osteosarcoma, Uterine neoplasms
PLCG1 3 / 31 Hemangiosarcoma, immune dysregulation, autoimmunity, and autoinflammation, Sezary syndrome
RB1 3 / 31 Osteosarcoma, Sezary syndrome, Small cell lung carcinoma
VEGFA 3 / 31 Hemangiosarcoma, Osteosarcoma, Uterine neoplasms
AMER1 2 / 31 Osteopathia striata with cranial sclerosis, Wilms tumor
AMOTL1 2 / 31 Craniofaciocardiohepatic syndrome, Tethered cord syndrome
BAP1 2 / 31 Nasopharyngeal carcinoma, Uterine neoplasms
BCOR 2 / 31 Osteosarcoma, Wilms tumor
BCORL1 2 / 31 Shukla-vernon syndrome, Wilms tumor
BRCA2 2 / 31 Small cell lung carcinoma, Wilms tumor
CCDC39 2 / 31 Ellis-van creveld syndrome, primary ciliary dyskinesia 14
CDKN1B 2 / 31 Sezary syndrome, Uterine neoplasms
CHD3 2 / 31 Sezary syndrome, snijders blok-campeau syndrome
CREBBP 2 / 31 Sezary syndrome, Small cell lung carcinoma
ERCC1 2 / 31 Nasopharyngeal carcinoma, Uterine neoplasms
IGF2 2 / 31 Hepatoblastoma, Wilms tumor
IL32 2 / 31 Cervicitis, Sezary syndrome
JUN 2 / 31 Hemangiosarcoma, Osteosarcoma
MGP 2 / 31 keutel syndrome, Vascular calcification
MMP2 2 / 31 Nasopharyngeal carcinoma, Osteosarcoma
MST1R 2 / 31 Nasopharyngeal carcinoma, Osteosarcoma
SF3B4 2 / 31 Acrofacial dysostosis, SF3B4-related acrofacial dysostosis
SMARCA4 2 / 31 Sezary syndrome, Small cell lung carcinoma
SOX2 2 / 31 Osteosarcoma, Small cell lung carcinoma
WT1 2 / 31 Osteosarcoma, Wilms tumor
ZDBF2 2 / 31 Nasopalpebral lipoma-coloboma syndrome, Small cell lung carcinoma
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 ⇵
Pathways in cancer
APC, CDKN2A, CTNNB1, KRAS, PTEN, TP53, CCND1, BRAF, GLI1, PRKACA, PRKACB, HRAS
 KEGG 56 / 533 4.7× 7.77e-23 9.27e-20 ✓ sig.
Prostate cancer
CTNNB1, KRAS, PTEN, TP53, CCND1, BRAF, HRAS, TGFA, AKT2, ERBB2, NFKBIA, PIK3CA
 KEGG 22 / 98 10.0× 2.26e-16 8.62e-14 ✓ sig.
Hepatocellular carcinoma
APC, CDKN2A, CTNNB1, KRAS, PTEN, TP53, CCND1, BRAF, HRAS, MYC, PLCG1, IGF2
 KEGG 27 / 170 7.1× 8.60e-16 3.03e-13 ✓ sig.
Breast cancer
APC, CTNNB1, KRAS, PTEN, TP53, CCND1, BRAF, HRAS, JUN, MYC, AKT2, ERBB2
 KEGG 25 / 148 7.5× 2.38e-15 7.81e-13 ✓ sig.
Endocrine resistance
CDKN2A, KRAS, TP53, CCND1, BRAF, PRKACA, PRKACB, HRAS, JUN, AKT2, ERBB2, MMP2
 KEGG 21 / 99 9.4× 3.78e-15 1.20e-12 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
KRAS, PTEN, BRAF, HRAS, KDR, PLCG1, VEGFA, TGFA, AKT2, ERBB2, ERBB3, PIK3CA
 KEGG 19 / 80 10.6× 8.73e-15 2.54e-12 ✓ sig.
Proteoglycans in cancer
CTNNB1, KRAS, TP53, CCND1, BRAF, PRKACA, PRKACB, HRAS, KDR, MYC, PLCG1, VEGFA
 KEGG 28 / 204 6.1× 1.16e-14 3.30e-12 ✓ sig.
Bladder cancer
CDKN2A, KRAS, TP53, CCND1, BRAF, HRAS, MYC, VEGFA, ERBB2, MMP2, EGFR, RB1
 KEGG 14 / 41 15.2× 1.23e-13 2.97e-11 ✓ sig.
Non-small cell lung cancer
CDKN2A, KRAS, TP53, CCND1, BRAF, HRAS, PLCG1, TGFA, AKT2, ERBB2, PIK3CA, EGFR
 KEGG 17 / 73 10.4× 3.31e-13 7.30e-11 ✓ sig.
Pancreatic cancer
CDKN2A, KRAS, TP53, CCND1, BRAF, VEGFA, TGFA, AKT2, ERBB2, PIK3CA, EGFR, RB1
 KEGG 17 / 77 9.8× 8.48e-13 1.75e-10 ✓ sig.
Human T-cell leukemia virus 1 infection
CDKN2A, KRAS, PTEN, TP53, CCND1, PRKACA, PRKACB, HRAS, JUN, MYC, AKT2, NFKBIA
 KEGG 27 / 224 5.4× 8.71e-13 1.79e-10 ✓ sig.
Gastric cancer
APC, CTNNB1, KRAS, TP53, CCND1, BRAF, HRAS, MYC, AKT2, ERBB2, PIK3CA, EGFR
 KEGG 22 / 150 6.5× 2.36e-12 4.50e-10 ✓ sig.
MicroRNAs in cancer
APC, CDKN2A, KRAS, PTEN, TP53, CCND1, HRAS, MYC, PLCG1, VEGFA, ERBB2, ERBB3
 KEGG 31 / 311 4.4× 2.76e-12 5.20e-10 ✓ sig.
Colorectal cancer
APC, CTNNB1, KRAS, TP53, CCND1, BRAF, HRAS, JUN, MYC, TGFA, AKT2, PIK3CA
 KEGG 17 / 87 8.7× 7.00e-12 1.24e-9 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
APC, CTNNB1, KRAS, HRAS, MYC, AKT2, PIK3CA, BMI1, SOX2, MAPK1, FGFR1, ID2
 KEGG 21 / 144 6.5× 8.49e-12 1.47e-9 ✓ 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
CTNNB1, KRAS, TP53, CCND1, JUN, MYC, VEGFA, VEGFC, BAP1, ERBB2, ERCC1, BTC
 GO:0008283 33 / 263 8.7× 1.46e-21 2.87e-18 ✓ sig.
positive regulation of transcription by RNA polymerase II
CDKN2A, CTNNB1, PTEN, TP53, NRF1, PPARGC1A, GLI1, CSF3, HRAS, JUN, MYC, VEGFA
 GO:0045944 66 / 1,208 3.8× 1.52e-21 2.97e-18 ✓ sig.
positive regulation of DNA-templated transcription
CDKN1C, CDKN2A, CTNNB1, TP53, PPARGC1A, GLI1, JUN, MYC, ARID1A, NFKBIA, TP63, BLM
 GO:0045893 49 / 778 4.4× 1.90e-18 2.38e-15 ✓ sig.
positive regulation of cell population proliferation
CTNNB1, PTEN, CCND1, GLI1, CSF3, FLT1, HRAS, KDR, MYC, VEGFA, VEGFC, IGF2
 GO:0008284 40 / 532 5.2× 8.84e-18 9.99e-15 ✓ sig.
negative regulation of transcription by RNA polymerase II
CDKN1C, CDKN2A, CTNNB1, TP53, CCND1, JUN, MYC, VEGFA, IGF2, PCNA, NFKBIA, TP63
 GO:0000122 54 / 1,002 3.7× 2.63e-17 2.67e-14 ✓ sig.
positive regulation of gene expression
CDKN2A, CTNNB1, KRAS, TP53, PPARGC1A, IL32, BRAF, HRAS, MYC, VEGFA, ERBB2, ERBB3
 GO:0010628 37 / 504 5.1× 3.64e-16 3.01e-13 ✓ sig.
heart development
CTNNB1, PTEN, TP53, CCDC39, TEK, PCNA, ERBB2, ERBB3, MMP2, SOD2, ADAMTS6, BCOR
 GO:0007507 27 / 273 6.8× 3.51e-15 2.42e-12 ✓ sig.
regulation of gene expression
CDKN2A, CTNNB1, GLI1, MYC, BAP1, NFKBIA, PIK3CA, BMI1, EZH2, LOX, MET, PHLDA2
 GO:0010468 32 / 402 5.5× 4.41e-15 2.96e-12 ✓ sig.
negative regulation of apoptotic process
CTNNB1, TP53, BRAF, JUN, KDR, MYC, TEK, VEGFA, AKT2, ERBB2, ERBB3, SOD2
 GO:0043066 35 / 524 4.6× 4.18e-14 2.40e-11 ✓ sig.
negative regulation of DNA-templated transcription
CDKN1C, CDKN2A, CTNNB1, TP53, JUN, BAP1, TP63, BCOR, EZH2, HDAC6, MECOM, NR1I2
 GO:0045892 38 / 631 4.2× 8.13e-14 4.45e-11 ✓ sig.
positive regulation of epithelial cell proliferation
HRAS, KDR, MYC, VEGFA, VEGFC, TGFA, ERBB2, ERBB3, EGFR, RUNX2, BMP6, NOTCH1
 GO:0050679 15 / 73 14.2× 1.16e-13 6.24e-11 ✓ sig.
neuron differentiation
CTNNB1, CCND1, ERBB2, ERBB3, EGFR, HDAC6, MET, RB1, RUNX2, SOX2, DNMT3A, ALDH1A2
 GO:0030182 23 / 222 7.2× 1.58e-13 8.25e-11 ✓ sig.
regulation of cell population proliferation
CTNNB1, TP53, BRAF, COL18A1, FLT1, HRAS, JUN, ERBB2, ERBB3, NFKBIA, EGFR, EZH2
 GO:0042127 21 / 201 7.2× 1.58e-12 6.82e-10 ✓ sig.
kidney development
CDKN1C, CTNNB1, TRAF3IP1, VEGFA, AMER1, ADAMTS6, COMT, WT1, TP73, ALDH1A2, BAG6, BMP6
 GO:0001822 18 / 146 8.5× 3.89e-12 1.56e-9 ✓ sig.
negative regulation of cell population proliferation
APC, CDKN2A, CTNNB1, PTEN, TP53, COL18A1, HRAS, JUN, BAP1, SOD2, TNFRSF8, RB1
 GO:0008285 29 / 444 4.5× 1.28e-11 4.53e-9 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hemangiosarcoma Uterine neoplasms 0.118 6 2.71e-12 3.13e-11 ✓ sig.
Endometrial hyperplasia Nasopharyngeal carcinoma 0.138 4 6.52e-10 6.03e-9 ✓ sig.
Cecal neoplasms Hemangiosarcoma 0.150 3 5.36e-9 4.53e-8 ✓ sig.
Curry-hall syndrome Weyers acrofacial dysostosis 0.500 2 2.53e-8 1.93e-7 ✓ sig.
Acrofacial dysostosis Curry-hall syndrome 0.400 2 5.06e-8 3.72e-7 ✓ sig.
Nasopharyngeal carcinoma Sezary syndrome 0.087 4 5.37e-8 3.93e-7 ✓ sig.
Cecal neoplasms Uterine neoplasms 0.075 3 5.54e-8 4.05e-7 ✓ sig.
Acrofacial dysostosis Weyers acrofacial dysostosis 0.333 2 1.52e-7 1.03e-6 ✓ sig.
Endometrial hyperplasia Hemangiosarcoma 0.115 3 1.60e-7 1.09e-6 ✓ sig.
Curry-hall syndrome Ellis-van creveld syndrome 0.200 2 3.04e-7 1.96e-6 ✓ sig.
Sezary syndrome Small cell lung carcinoma 0.044 5 4.70e-7 2.94e-6 ✓ sig.
Hemangiosarcoma Osteosarcoma 0.056 4 4.97e-7 3.10e-6 ✓ sig.
Endometrial hyperplasia Sezary syndrome 0.086 3 5.72e-7 3.51e-6 ✓ sig.
Ellis-van creveld syndrome Weyers acrofacial dysostosis 0.182 2 9.11e-7 5.38e-6 ✓ sig.
Acrofacial dysostosis Ellis-van creveld syndrome 0.167 2 1.82e-6 1.02e-5 ✓ sig.
Cecal neoplasms Endometrial hyperplasia 0.154 2 2.28e-6 1.26e-5 ✓ sig.
Osteopathia striata with cranial sclerosis Wilms tumor 0.061 2 4.18e-6 2.21e-5 ✓ sig.
Hepatoblastoma Wilms tumor 0.057 2 2.50e-5 1.17e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.500 1 6.49e-5 2.32e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Craniopharyngioma CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Hairy cell leukemia Tethered cord syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Craniopharyngioma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Craniopharyngioma Hairy cell leukemia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Craniofaciocardiohepatic syndrome Tethered cord syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Vascular calcification 0.333 1 1.30e-4 3.91e-4 ✓ sig.
keutel syndrome Vascular calcification 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Vascular calcification 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Osteopathia striata with cranial sclerosis 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Intellectual developmental disorder dysmorphic ocular microcephaly peripheral Weyers acrofacial dysostosis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Weyers acrofacial dysostosis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Craniopharyngioma Vascular calcification 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Craniopharyngioma Tethered cord syndrome 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Craniopharyngioma Osteopathia striata with cranial sclerosis 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Osteopathia striata with cranial sclerosis Vascular calcification 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Cecal neoplasms Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Acrofacial dysostosis SF3B4-related acrofacial dysostosis 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cecal neoplasms CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy 0.200 1 2.60e-4 6.48e-4 ✓ sig.
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy Hepatoblastoma 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Hepatoblastoma Intellectual developmental disorder dysmorphic ocular microcephaly peripheral 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Craniopharyngioma Weyers acrofacial dysostosis 0.200 1 3.90e-4 8.64e-4 ✓ 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.
Craniopharyngioma Hepatoblastoma 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Ellis-van creveld syndrome primary ciliary dyskinesia 14 0.100 1 5.84e-4 1.15e-3 ✓ sig.
Bowen’s disease Cecal neoplasms 0.125 1 1.04e-3 1.74e-3 ✓ sig.
Hemangiosarcoma immune dysregulation, autoimmunity, and autoinflammation 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Cervicitis Sezary syndrome 0.036 1 1.75e-3 2.61e-3 ✓ sig.
Sezary syndrome snijders blok-campeau syndrome 0.036 1 1.75e-3 2.61e-3 ✓ sig.
immune dysregulation, autoimmunity, and autoinflammation Sezary syndrome 0.036 1 1.75e-3 2.61e-3 ✓ sig.
Shukla-vernon syndrome Wilms tumor 0.030 1 2.08e-3 2.97e-3 ✓ sig.
Nasopalpebral lipoma-coloboma syndrome Small cell lung carcinoma 0.011 1 5.91e-3 7.12e-3 ✓ sig.