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 116

12 diseases · 31 shared-gene connections
12 Diseases
55 Unique genes
0.298 Avg. similarity score
Colon dysplasia Most-connected disease (8 links)
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Disease Searched: Ollier disease/ dyschondroplasia 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 ⇵
Colon dysplasia 8 8 2
Metaphyseal enchondromatosis 8 8 1
Periosteal chondroma 8 8 1
Pancreatic serous cystadenocarcinoma 7 7 1
Brain cancer 6 6 10
Ollier disease/ dyschondroplasia 6 6 1
Ovarian gynandroblastoma 6 6 3
Dysembryoplastic neuroepithelial tumor 5 5 4
Angiokeratoma 3 3 5
Blepharophimosis-ptosis-epicanthus inversus syndrome 2 2 1
Ovarian sex cord-stromal tumor 2 2 4
Brain neoplasms 1 1 38

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

Gene ⇵ Member diseases ⇵ Linked diseases
IDH1 9 / 12 Angiokeratoma, Brain cancer, Colon dysplasia, Dysembryoplastic neuroepithelial tumor and 5 more
FOXL2 3 / 12 Blepharophimosis-ptosis-epicanthus inversus syndrome, Ovarian gynandroblastoma, Ovarian sex cord-stromal tumor
APOBEC3C 2 / 12 Brain cancer, Brain neoplasms
CCT6B 2 / 12 Brain cancer, Brain neoplasms
DICER1 2 / 12 Ovarian gynandroblastoma, Ovarian sex cord-stromal tumor
FCHO2 2 / 12 Brain cancer, Brain neoplasms
FOXN3 2 / 12 Brain cancer, Brain neoplasms
TP53 2 / 12 Brain cancer, Colon dysplasia
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 ⇵
Non-small cell lung cancer
ALK, CCND1, CDK4, CDKN2A, EML4, HRAS, TP53, FOXO3, PIK3CA, BRAF
 KEGG 10 / 73 29.9× 8.55e-13 1.66e-10 ✓ sig.
Pathways in cancer
TERT, ALK, CCND1, CDK4, CDKN2A, DAPK1, DLL1, EML4, HES5, HRAS, IL2, PTCH1
 KEGG 19 / 533 7.8× 9.12e-13 1.75e-10 ✓ sig.
Bladder cancer
CCND1, CDK4, CDKN2A, DAPK1, HRAS, VEGFA, TP53, BRAF
 KEGG 8 / 41 42.6× 9.68e-12 1.47e-9 ✓ sig.
Pancreatic cancer
CCND1, CDK4, CDKN2A, RELA, TGFBR2, VEGFA, TP53, PIK3CA, BRAF
 KEGG 9 / 77 25.5× 5.68e-11 7.12e-9 ✓ sig.
Chronic myeloid leukemia
CCND1, CDK4, CDKN2A, HRAS, RELA, TGFBR2, TP53, PIK3CA, BRAF
 KEGG 9 / 77 25.5× 5.68e-11 7.12e-9 ✓ sig.
Cellular senescence
CCND1, CDK4, CDKN2A, HRAS, RELA, SIRT1, TGFBR2, TP53, FOXO3, PIK3CA
 KEGG 10 / 157 13.9× 1.93e-9 1.68e-7 ✓ sig.
Human T-cell leukemia virus 1 infection
TERT, CCND1, CDK4, CDKN2A, HRAS, IL2, ITGB2, RELA, TGFBR2, TP53, PIK3CA
 KEGG 11 / 224 10.7× 4.33e-9 3.49e-7 ✓ sig.
Endocrine resistance
CCND1, CDK4, CDKN2A, DLL1, HRAS, TP53, PIK3CA, BRAF
 KEGG 8 / 99 17.6× 1.42e-8 1.01e-6 ✓ sig.
Melanoma
CCND1, CDK4, CDKN2A, HRAS, TP53, PIK3CA, BRAF
 KEGG 7 / 73 20.9× 3.67e-8 2.34e-6 ✓ sig.
Glioma
CCND1, CDK4, CDKN2A, HRAS, TP53, PIK3CA, BRAF
 KEGG 7 / 76 20.1× 4.88e-8 2.98e-6 ✓ sig.
Hepatocellular carcinoma
TERT, CCND1, CDK4, CDKN2A, HRAS, TGFBR2, TP53, PIK3CA, BRAF
 KEGG 9 / 170 11.6× 6.71e-8 3.94e-6 ✓ sig.
FoxO signaling pathway
CCND1, HRAS, SIRT1, SOD2, TGFBR2, FOXO3, PIK3CA, BRAF
 KEGG 8 / 133 13.1× 1.44e-7 7.69e-6 ✓ sig.
Longevity regulating pathway
HRAS, RELA, SIRT1, SOD2, TP53, FOXO3, PIK3CA
 KEGG 7 / 90 17.0× 1.59e-7 8.38e-6 ✓ sig.
Endometrial cancer
CCND1, HRAS, TP53, FOXO3, PIK3CA, BRAF
 KEGG 6 / 59 22.2× 2.61e-7 1.30e-5 ✓ sig.
Proteoglycans in cancer
CCND1, HRAS, IQGAP1, PTCH1, SMO, VEGFA, TP53, PIK3CA, BRAF
 KEGG 9 / 204 9.6× 3.19e-7 1.54e-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 ⇵
negative regulation of transcription by RNA polymerase II
FOXL2, AMOT, CCND1, CDKN2A, HES5, NRARP, PCNA, PTCH1, RELA, SIRT1, SMO, SOX2
 GO:0000122 20 / 1,002 6.8× 2.70e-12 1.17e-9 ✓ sig.
positive regulation of cell population proliferation
CCND1, CDK4, DLL1, HES5, HRAS, IL2, RELA, S100B, SIRT1, SMO, TGFBR2, VEGFA
 GO:0008284 14 / 532 8.9× 2.89e-10 7.92e-8 ✓ sig.
regulation of cell population proliferation
ALK, HRAS, PTCH1, SIRT1, TGFBR2, YAP1, TP53, NF2, BRAF
 GO:0042127 9 / 201 15.2× 6.68e-9 1.25e-6 ✓ sig.
negative regulation of epithelial cell differentiation
CCND1, DLL1, SMO, YAP1
 GO:0030857 4 / 17 79.9× 1.55e-7 1.84e-5 ✓ sig.
cellular response to hypoxia
TERT, S100B, SIRT1, SOX2, VEGFA, TP53, FOXO3
 GO:0071456 7 / 139 17.1× 1.63e-7 1.91e-5 ✓ sig.
negative regulation of apoptotic process
TERT, DAPK1, IL2, MGMT, RELA, SIRT1, SMO, SOD2, VEGFA, TP53, BRAF
 GO:0043066 11 / 524 7.1× 2.97e-7 3.16e-5 ✓ sig.
negative regulation of neuron apoptotic process
TERT, CCND1, HRAS, SIRT1, SOD2, PIK3CA, BRAF
 GO:0043524 7 / 160 14.9× 4.25e-7 4.25e-5 ✓ sig.
response to xenobiotic stimulus
CCND1, CDK4, PTCH1, RELA, SOD2, TGFBR2, TP53, FOXO3
 GO:0009410 8 / 248 11.0× 6.11e-7 5.75e-5 ✓ sig.
neuronal stem cell population maintenance
DLL1, HES5, SOX2, FOXO3
 GO:0097150 4 / 24 56.6× 6.83e-7 6.29e-5 ✓ sig.
vasculogenesis
AMOT, SMO, TGFBR2, VEGFA, YAP1
 GO:0001570 5 / 63 27.0× 1.13e-6 9.51e-5 ✓ sig.
positive regulation of DNA-templated transcription
FOXL2, CDKN2A, HES5, PTCH1, RELA, SMO, SOX2, SPP1, YAP1, TP53, FOXO3, NSD1
 GO:0045893 12 / 778 5.2× 2.10e-6 1.57e-4 ✓ sig.
regulation of stem cell proliferation
TGFBR2, YAP1, NF2
 GO:0072091 3 / 11 92.7× 3.91e-6 2.60e-4 ✓ sig.
positive regulation of apoptotic process
FOXL2, CDKN2A, DAPK1, S100B, SIRT1, TGM2, TP53, FOXO3
 GO:0043065 8 / 326 8.3× 4.70e-6 3.02e-4 ✓ sig.
negative regulation of gene expression
HRAS, SIRT1, SMO, VEGFA, YAP1, TP53, PIK3CA, DICER1
 GO:0010629 8 / 339 8.0× 6.26e-6 3.79e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
FOXL2, CDKN2A, DLL1, HES5, HRAS, IL2, RELA, SIRT1, SMO, SOX2, VEGFA, YAP1
 GO:0045944 14 / 1,208 3.9× 7.34e-6 4.28e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Brain cancer Brain neoplasms 0.091 4 3.85e-9 3.17e-8 ✓ sig.
Ovarian gynandroblastoma Ovarian sex cord-stromal tumor 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Pancreatic serous cystadenocarcinoma Periosteal chondroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Metaphyseal enchondromatosis Periosteal chondroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Metaphyseal enchondromatosis Pancreatic serous cystadenocarcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon dysplasia Ollier disease/ dyschondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon dysplasia Pancreatic serous cystadenocarcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon dysplasia Periosteal chondroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Colon dysplasia Metaphyseal enchondromatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Metaphyseal enchondromatosis Ollier disease/ dyschondroplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ollier disease/ dyschondroplasia Periosteal chondroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ollier disease/ dyschondroplasia Pancreatic serous cystadenocarcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Metaphyseal enchondromatosis Ovarian gynandroblastoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Colon dysplasia Ovarian gynandroblastoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Ovarian gynandroblastoma Periosteal chondroma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Ovarian gynandroblastoma Pancreatic serous cystadenocarcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysembryoplastic neuroepithelial tumor Metaphyseal enchondromatosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysembryoplastic neuroepithelial tumor Ollier disease/ dyschondroplasia 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysembryoplastic neuroepithelial tumor Pancreatic serous cystadenocarcinoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysembryoplastic neuroepithelial tumor Periosteal chondroma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Colon dysplasia Dysembryoplastic neuroepithelial tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Blepharophimosis-ptosis-epicanthus inversus syndrome Ovarian gynandroblastoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Angiokeratoma Metaphyseal enchondromatosis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Blepharophimosis-ptosis-epicanthus inversus syndrome Ovarian sex cord-stromal tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Angiokeratoma Periosteal chondroma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Angiokeratoma Colon dysplasia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Brain cancer Ollier disease/ dyschondroplasia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Brain cancer Pancreatic serous cystadenocarcinoma 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Brain cancer Periosteal chondroma 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Brain cancer Colon dysplasia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Brain cancer Metaphyseal enchondromatosis 0.100 1 5.81e-4 1.00e-3 ✓ sig.