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 143

9 diseases · 16 shared-gene connections
9 Diseases
28 Unique genes
0.219 Avg. similarity score
Buschke-ollendorff syndrome Most-connected disease (5 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 ⇵
Buschke-ollendorff syndrome 5 5 1
Cerebral arteriovenous malformations 5 5 22
Dermatofibrosis lenticularis disseminata 5 5 1
Osteopoikilosis 5 5 1
Tietz syndrome 5 5 5
12q14 microdeletion syndrome 4 4 2
Cerebellar vermis atrophy 1 1 1
neurodevelopmental disorder with microcephaly, ataxia, and seizures 1 1 1
qualitative platelet defect 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
LEMD3 6 / 9 12q14 microdeletion syndrome, Buschke-ollendorff syndrome, Cerebral arteriovenous malformations, Dermatofibrosis lenticularis disseminata and 2 more
ABCC4 2 / 9 qualitative platelet defect, Tietz syndrome
SARS1 2 / 9 Cerebral arteriovenous malformations, neurodevelopmental disorder with microcephaly, ataxia, and seizures
SYN3 2 / 9 Cerebellar vermis atrophy, Cerebral arteriovenous malformations
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 ⇵
Melanoma
BRAF, EGFR, KRAS, MITF
 KEGG 4 / 73 23.5× 2.30e-5 6.70e-4 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
BRAF, EGFR, KRAS, IL6
 KEGG 4 / 80 21.4× 3.31e-5 9.07e-4 ✓ sig.
Endocrine resistance
BRAF, EGFR, KRAS, NOTCH4
 KEGG 4 / 99 17.3× 7.64e-5 1.80e-3 ✓ sig.
MAP2K and MAPK activation
BRAF, IL17RD, KRAS
 Reactome 3 / 40 32.2× 1.06e-4 2.36e-3 ✓ sig.
Bladder cancer
BRAF, EGFR, KRAS
 KEGG 3 / 41 31.4× 1.14e-4 2.49e-3 ✓ sig.
Pathways in cancer
BRAF, EGFR, GLI2, KRAS, NOTCH4, IL6, MITF
 KEGG 7 / 533 5.6× 1.71e-4 3.45e-3 ✓ sig.
EGFR Transactivation by Gastrin
EGFR, KRAS
 Reactome 2 / 9 95.3× 1.87e-4 3.72e-3 ✓ sig.
FoxO signaling pathway
BRAF, EGFR, KRAS, IL6
 KEGG 4 / 133 12.9× 2.39e-4 4.50e-3 ✓ sig.
Endometrial cancer
BRAF, EGFR, KRAS
 KEGG 3 / 59 21.8× 3.38e-4 5.89e-3 ✓ sig.
Breast cancer
BRAF, EGFR, KRAS, NOTCH4
 KEGG 4 / 148 11.6× 3.60e-4 6.18e-3 ✓ sig.
GRB2 events in EGFR signaling
EGFR, KRAS
 Reactome 2 / 13 66.0× 4.02e-4 6.74e-3 ✓ sig.
SHC1 events in EGFR signaling
EGFR, KRAS
 Reactome 2 / 14 61.3× 4.69e-4 7.58e-3 ✓ sig.
Constitutive Signaling by EGFRvIII
EGFR, KRAS
 Reactome 2 / 15 57.2× 5.40e-4 8.45e-3 ✓ sig.
MAPK signaling pathway
BRAF, CACNA1H, EGFR, KRAS, MAP4K4
 KEGG 5 / 299 7.2× 5.68e-4 8.79e-3 ✓ sig.
Signaling by ERBB2 ECD mutants
EGFR, KRAS
 Reactome 2 / 16 53.6× 6.16e-4 9.39e-3 ✓ 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 peptidyl-serine phosphorylation
BRAF, EGFR, PDCD10, IL6
 GO:0033138 4 / 20 133× 1.92e-8 3.01e-6 ✓ sig.
negative regulation of apoptotic process
HMGA2, BRAF, EGFR, MAP4K4, PDCD10, IL6, MITF
 GO:0043066 7 / 524 8.9× 9.29e-6 4.93e-4 ✓ sig.
MAPK cascade
BRAF, EGFR, KRAS, MAP4K4
 GO:0000165 4 / 147 18.2× 6.50e-5 2.19e-3 ✓ sig.
positive regulation of T-helper 2 cell cytokine production
NLRP3, IL6
 GO:2000553 2 / 9 148× 7.74e-5 2.50e-3 ✓ sig.
positive regulation of gene expression
HMGA2, BRAF, KRAS, PDCD10, IL6, MITF
 GO:0010628 6 / 504 7.9× 8.49e-5 2.68e-3 ✓ sig.
synaptic vesicle clustering
CDH2, SYN3
 GO:0097091 2 / 12 111× 1.42e-4 3.92e-3 ✓ sig.
regulation of synaptic transmission, GABAergic
KRAS, SYN3
 GO:0032228 2 / 14 95.3× 1.95e-4 4.96e-3 ✓ sig.
regulation of cell population proliferation
BRAF, EGFR, ENG, MITF
 GO:0042127 4 / 201 13.3× 2.17e-4 5.34e-3 ✓ sig.
positive regulation of protein serine/threonine kinase activity
HMGA2, PDCD10
 GO:0071902 2 / 15 89.0× 2.25e-4 5.47e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
HMGA2, EGFR, ENG, GLI2, NLRP3, NOTCH4, IL6, MITF
 GO:0045944 8 / 1,208 4.4× 2.89e-4 6.53e-3 ✓ sig.
cellular response to virus
GLI2, NLRP3, IL6
 GO:0098586 3 / 89 22.5× 3.14e-4 6.93e-3 ✓ sig.
striated muscle cell differentiation
CDH2, KRAS
 GO:0051146 2 / 20 66.7× 4.05e-4 8.28e-3 ✓ sig.
epithelial tube branching involved in lung morphogenesis
HMGA2, KRAS
 GO:0060441 2 / 20 66.7× 4.05e-4 8.28e-3 ✓ sig.
positive regulation of glial cell proliferation
KRAS, IL6
 GO:0060252 2 / 22 60.7× 4.91e-4 9.44e-3 ✓ sig.
stress fiber assembly
BRAF, PDCD10
 GO:0043149 2 / 24 55.6× 5.85e-4 1.07e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Buschke-ollendorff syndrome Dermatofibrosis lenticularis disseminata 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Buschke-ollendorff syndrome Osteopoikilosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dermatofibrosis lenticularis disseminata Osteopoikilosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
12q14 microdeletion syndrome Buschke-ollendorff syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
12q14 microdeletion syndrome Dermatofibrosis lenticularis disseminata 0.333 1 1.30e-4 3.90e-4 ✓ sig.
12q14 microdeletion syndrome Osteopoikilosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Buschke-ollendorff syndrome Tietz syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Dermatofibrosis lenticularis disseminata Tietz syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Osteopoikilosis Tietz syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
qualitative platelet defect Tietz syndrome 0.143 1 6.49e-4 1.22e-3 ✓ sig.
12q14 microdeletion syndrome Tietz syndrome 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Buschke-ollendorff syndrome Cerebral arteriovenous malformations 0.043 1 1.43e-3 2.21e-3 ✓ sig.
Cerebellar vermis atrophy Cerebral arteriovenous malformations 0.043 1 1.43e-3 2.21e-3 ✓ sig.
Cerebral arteriovenous malformations Dermatofibrosis lenticularis disseminata 0.043 1 1.43e-3 2.21e-3 ✓ sig.
Cerebral arteriovenous malformations neurodevelopmental disorder with microcephaly, ataxia, and seizures 0.043 1 1.43e-3 2.21e-3 ✓ sig.
Cerebral arteriovenous malformations Osteopoikilosis 0.043 1 1.43e-3 2.21e-3 ✓ sig.