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 71

13 diseases · 40 shared-gene connections
13 Diseases
112 Unique genes
0.224 Avg. similarity score
17q11.2 microduplication syndrome Most-connected disease (10 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 ⇵
17q11.2 microduplication syndrome 10 10 1
Cervical lymphadenopathy 10 10 1
Watson syndrome 10 10 1
Middle aortic syndrome 7 7 4
Cafe-au-lait spots 6 6 6
Neurofibromatosis 6 6 4
Neurofibromatosis-noonan syndrome 6 6 4
neurofibromatosis type 1 6 6 1
17q11 microdeletion syndrome 5 5 2
Moyamoya angiopathy 5 5 36
Embryonal nuclear cataract 4 4 6
legius syndrome 3 3 1
Moyamoya disease 2 2 62

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

Gene ⇵ Member diseases ⇵ Linked diseases
NF1 12 / 13 17q11 microdeletion syndrome, 17q11.2 microduplication syndrome, Cafe-au-lait spots, Cervical lymphadenopathy and 8 more
SPRED1 4 / 13 Cafe-au-lait spots, legius syndrome, Neurofibromatosis, Neurofibromatosis-noonan syndrome
RNF213 3 / 13 Middle aortic syndrome, Moyamoya angiopathy, Moyamoya disease
BRCC3 2 / 13 Moyamoya angiopathy, Moyamoya disease
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 ⇵
Chronic myeloid leukemia
SOS1, TP53, ABL1, PIK3CD, SMAD4, MAP2K2, PTPN11
 KEGG 7 / 77 9.7× 7.13e-6 2.53e-4 ✓ sig.
RUNX3 regulates CDKN1A transcription
TP53, SMAD4, ZFHX3
 Reactome 3 / 7 46.0× 2.69e-5 7.60e-4 ✓ sig.
Renal cell carcinoma
SOS1, CUL2, PIK3CD, RAP1A, MAP2K2, PTPN11
 KEGG 6 / 70 9.2× 4.64e-5 1.20e-3 ✓ sig.
Phospholipase D signaling pathway
SOS1, GNAS, DNM2, PIK3CD, DNM3, RAPGEF4, MAP2K2, PTPN11
 KEGG 8 / 149 5.8× 7.44e-5 1.76e-3 ✓ sig.
Neurotrophin signaling pathway
SOS1, TP53, ABL1, PIK3CD, RAP1A, MAP2K2, PTPN11
 KEGG 7 / 120 6.3× 1.27e-4 2.72e-3 ✓ sig.
Natural killer cell mediated cytotoxicity
SOS1, PIK3CD, FAS, HLA-A, LAT2, MAP2K2, PTPN11
 KEGG 7 / 133 5.6× 2.41e-4 4.52e-3 ✓ sig.
Endocrine resistance
SOS1, GNAS, TP53, JAG1, PIK3CD, MAP2K2
 KEGG 6 / 99 6.5× 3.19e-4 5.62e-3 ✓ sig.
Proteoglycans in cancer
SOS1, TP53, PIK3CD, FAS, TWIST1, WNT9A, MAP2K2, PTPN11
 KEGG 8 / 204 4.2× 6.34e-4 9.61e-3 ✓ sig.
Colorectal cancer
SOS1, TP53, PIK3CD, SMAD4, MAP2K2
 KEGG 5 / 87 6.2× 1.30e-3 1.65e-2 ✓ sig.
Ras signaling pathway
NF1, SOS1, ABL1, PIK3CD, FLT1, RAP1A, MAP2K2, PTPN11
 KEGG 8 / 237 3.6× 1.67e-3 2.00e-2 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
NF1, SPRED1
 Reactome 2 / 7 30.6× 1.76e-3 2.07e-2 ✓ sig.
MAPK signaling pathway
NF1, SOS1, CACNA1S, TP53, MAP3K11, FAS, FLT1, RAP1A, MAP2K2
 KEGG 9 / 299 3.2× 1.90e-3 2.19e-2 ✓ sig.
Endometrial cancer
SOS1, TP53, PIK3CD, MAP2K2
 KEGG 4 / 59 7.3× 2.20e-3 2.44e-2 ✓ sig.
Breast cancer
SOS1, TP53, JAG1, PIK3CD, WNT9A, MAP2K2
 KEGG 6 / 148 4.3× 2.59e-3 2.77e-2 ✓ sig.
Gastric cancer
SOS1, TP53, PIK3CD, SMAD4, WNT9A, MAP2K2
 KEGG 6 / 150 4.3× 2.77e-3 2.91e-2 ✓ 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 ⇵
regulation of cell population proliferation
NF1, SOS1, TP53, JAG1, ABL1, PID1, SMAD4, CFDP1, FLT1, ENG, NF2
 GO:0042127 11 / 201 9.1× 3.45e-8 4.95e-6 ✓ sig.
negative regulation of Schwann cell proliferation
NF1, DICER1, NF2
 GO:0010626 3 / 8 62.6× 1.15e-5 5.80e-4 ✓ sig.
atrioventricular canal development
GATA6, SMAD4, PTPN11
 GO:0036302 3 / 11 45.5× 3.34e-5 1.33e-3 ✓ sig.
Schwann cell proliferation
NF1, NF2
 GO:0014010 2 / 3 111× 1.06e-4 3.17e-3 ✓ sig.
negative regulation of cell-cell adhesion
JAG1, ABL1, NF2
 GO:0022408 3 / 17 29.4× 1.34e-4 3.77e-3 ✓ sig.
cardiac neural crest cell development involved in outflow tract morphogenesis
JAG1, TWIST1
 GO:0061309 2 / 4 83.4× 2.12e-4 5.26e-3 ✓ sig.
Schwann cell development
NF1, SOS1, MAP2K2
 GO:0014044 3 / 20 25.0× 2.22e-4 5.43e-3 ✓ sig.
negative regulation of cell-matrix adhesion
NF1, JAG1, NF2
 GO:0001953 3 / 22 22.8× 2.97e-4 6.67e-3 ✓ sig.
synaptic vesicle budding from presynaptic endocytic zone membrane
DNM2, DNM3
 GO:0016185 2 / 5 66.7× 3.52e-4 7.48e-3 ✓ sig.
B cell receptor signaling pathway
SOS1, ABL1, PIK3CD, LAT2
 GO:0050853 4 / 56 11.9× 3.53e-4 7.49e-3 ✓ sig.
actin cytoskeleton organization
NF1, ABL1, CDC42BPG, DIAPH1, FMNL2, PHACTR1, NF2
 GO:0030036 7 / 234 5.0× 5.25e-4 9.89e-3 ✓ sig.
negative regulation of neurotransmitter secretion
NF1, PNKD
 GO:0046929 2 / 6 55.6× 5.26e-4 9.90e-3 ✓ sig.
cardiac atrium morphogenesis
SOS1, ENG
 GO:0003209 2 / 6 55.6× 5.26e-4 9.90e-3 ✓ sig.
outflow tract septum morphogenesis
GATA6, SMAD4, ENG
 GO:0003148 3 / 28 17.9× 6.16e-4 1.11e-2 ✓ sig.
positive regulation of neuron apoptotic process
NF1, TP53, ABL1, MAP3K11
 GO:0043525 4 / 65 10.3× 6.25e-4 1.12e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Neurofibromatosis Neurofibromatosis-noonan syndrome 0.286 2 3.04e-7 2.06e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis 0.222 2 7.59e-7 4.79e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis-noonan syndrome 0.222 2 7.59e-7 4.79e-6 ✓ sig.
Middle aortic syndrome Moyamoya angiopathy 0.051 2 3.18e-5 1.55e-4 ✓ sig.
17q11.2 microduplication syndrome Cervical lymphadenopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
17q11.2 microduplication syndrome Watson syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
17q11.2 microduplication syndrome neurofibromatosis type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
neurofibromatosis type 1 Watson syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cervical lymphadenopathy Watson syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cervical lymphadenopathy neurofibromatosis type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Middle aortic syndrome Moyamoya disease 0.031 2 9.52e-5 3.40e-4 ✓ sig.
17q11 microdeletion syndrome neurofibromatosis type 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
17q11 microdeletion syndrome 17q11.2 microduplication syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
17q11 microdeletion syndrome Watson syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
17q11 microdeletion syndrome Cervical lymphadenopathy 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Neurofibromatosis-noonan syndrome Watson syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Middle aortic syndrome Watson syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Middle aortic syndrome neurofibromatosis type 1 0.200 1 2.60e-4 6.40e-4 ✓ sig.
17q11.2 microduplication syndrome Neurofibromatosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Neurofibromatosis Watson syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
17q11.2 microduplication syndrome Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
legius syndrome Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
legius syndrome Neurofibromatosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
17q11.2 microduplication syndrome Middle aortic syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cervical lymphadenopathy Middle aortic syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Embryonal nuclear cataract Watson syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
17q11.2 microduplication syndrome Cafe-au-lait spots 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cafe-au-lait spots Cervical lymphadenopathy 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cafe-au-lait spots Watson syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
17q11.2 microduplication syndrome Embryonal nuclear cataract 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cervical lymphadenopathy Embryonal nuclear cataract 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Cafe-au-lait spots legius syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Embryonal nuclear cataract neurofibromatosis type 1 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Moyamoya angiopathy Moyamoya disease 0.031 3 4.04e-4 8.83e-4 ✓ sig.
17q11 microdeletion syndrome Middle aortic syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Moyamoya angiopathy Watson syndrome 0.027 1 2.34e-3 3.23e-3 ✓ sig.
Cervical lymphadenopathy Moyamoya angiopathy 0.027 1 2.34e-3 3.23e-3 ✓ sig.
17q11.2 microduplication syndrome Moyamoya angiopathy 0.027 1 2.34e-3 3.23e-3 ✓ sig.