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 95

11 diseases · 33 shared-gene connections
11 Diseases
53 Unique genes
0.209 Avg. similarity score
17q11.2 microduplication syndrome Most-connected disease (9 links)
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Disease Searched: Cervical lymphadenopathy 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 9 9 1
Cervical lymphadenopathy 9 9 1
Watson syndrome 9 9 1
Neurofibromatosis 7 7 4
Cafe-au-lait spots 6 6 6
Neurofibromatosis-noonan syndrome 6 6 4
17q11 microdeletion syndrome 5 5 2
Middle aortic syndrome 5 5 4
Moyamoya angiopathy 4 4 36
Embryonal nuclear cataract 3 3 6
legius syndrome 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NF1 10 / 11 17q11 microdeletion syndrome, 17q11.2 microduplication syndrome, Cafe-au-lait spots, Cervical lymphadenopathy and 6 more
SPRED1 4 / 11 Cafe-au-lait spots, legius syndrome, Neurofibromatosis, Neurofibromatosis-noonan syndrome
RNF213 2 / 11 Middle aortic syndrome, Moyamoya angiopathy
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 20.6× 4.10e-8 2.88e-6 ✓ sig.
RUNX3 regulates CDKN1A transcription
TP53, SMAD4, ZFHX3
 Reactome 3 / 7 97.1× 2.81e-6 1.13e-4 ✓ sig.
Endocrine resistance
SOS1, GNAS, TP53, JAG1, PIK3CD, MAP2K2
 KEGG 6 / 99 13.7× 4.52e-6 1.70e-4 ✓ sig.
Renal cell carcinoma
SOS1, CUL2, PIK3CD, MAP2K2, PTPN11
 KEGG 5 / 70 16.2× 1.34e-5 4.18e-4 ✓ sig.
Neurotrophin signaling pathway
SOS1, TP53, ABL1, PIK3CD, MAP2K2, PTPN11
 KEGG 6 / 120 11.3× 1.37e-5 4.24e-4 ✓ sig.
Colorectal cancer
SOS1, TP53, PIK3CD, SMAD4, MAP2K2
 KEGG 5 / 87 13.0× 3.88e-5 1.01e-3 ✓ sig.
Phospholipase D signaling pathway
SOS1, GNAS, DNM2, PIK3CD, MAP2K2, PTPN11
 KEGG 6 / 149 9.1× 4.68e-5 1.18e-3 ✓ sig.
Endometrial cancer
SOS1, TP53, PIK3CD, MAP2K2
 KEGG 4 / 59 15.4× 1.29e-4 2.67e-3 ✓ sig.
Growth hormone synthesis, secretion and action
SOS1, GNAS, CACNA1S, PIK3CD, MAP2K2
 KEGG 5 / 122 9.3× 1.94e-4 3.71e-3 ✓ sig.
Non-small cell lung cancer
SOS1, TP53, PIK3CD, MAP2K2
 KEGG 4 / 73 12.4× 2.94e-4 5.16e-3 ✓ sig.
Glioma
SOS1, TP53, PIK3CD, MAP2K2
 KEGG 4 / 76 11.9× 3.43e-4 5.86e-3 ✓ sig.
Chemical carcinogenesis - receptor activation
SOS1, GNAS, CACNA1S, JAG1, PIK3CD, MAP2K2
 KEGG 6 / 215 6.3× 3.49e-4 5.95e-3 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
NF1, SPRED1
 Reactome 2 / 7 64.7× 3.96e-4 6.57e-3 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
NF1, SOS1, PIK3CD, MAP2K2
 KEGG 4 / 80 11.3× 4.17e-4 6.85e-3 ✓ sig.
Breast cancer
SOS1, TP53, JAG1, PIK3CD, MAP2K2
 KEGG 5 / 148 7.7× 4.73e-4 7.56e-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 ⇵
regulation of cell population proliferation
NF1, SOS1, TP53, JAG1, ABL1, PID1, SMAD4, NF2
 GO:0042127 8 / 201 14.0× 9.12e-8 1.11e-5 ✓ sig.
negative regulation of Schwann cell proliferation
NF1, DICER1, NF2
 GO:0010626 3 / 8 132× 1.19e-6 9.61e-5 ✓ sig.
atrioventricular canal development
GATA6, SMAD4, PTPN11
 GO:0036302 3 / 11 96.2× 3.50e-6 2.27e-4 ✓ sig.
negative regulation of cell-cell adhesion
JAG1, ABL1, NF2
 GO:0022408 3 / 17 62.2× 1.42e-5 6.93e-4 ✓ sig.
Schwann cell proliferation
NF1, NF2
 GO:0014010 2 / 3 235× 2.36e-5 1.02e-3 ✓ sig.
Schwann cell development
NF1, SOS1, MAP2K2
 GO:0014044 3 / 20 52.9× 2.37e-5 1.03e-3 ✓ sig.
negative regulation of cell-matrix adhesion
NF1, JAG1, NF2
 GO:0001953 3 / 22 48.1× 3.19e-5 1.29e-3 ✓ sig.
positive regulation of neuron apoptotic process
NF1, TP53, ABL1, MAP3K11
 GO:0043525 4 / 65 21.7× 3.43e-5 1.36e-3 ✓ sig.
negative regulation of neurotransmitter secretion
NF1, PNKD
 GO:0046929 2 / 6 118× 1.18e-4 3.42e-3 ✓ sig.
cellular response to ionizing radiation
TP53, EEF1D, BRCC3
 GO:0071479 3 / 41 25.8× 2.13e-4 5.27e-3 ✓ sig.
regulation of MAPK cascade
NF1, SPRED1, PTPN11
 GO:0043408 3 / 41 25.8× 2.13e-4 5.27e-3 ✓ sig.
positive regulation of protein localization to early endosome
SORL1, NF2
 GO:1902966 2 / 10 70.5× 3.50e-4 7.51e-3 ✓ sig.
negative regulation of mitophagy
TP53, FBXL4
 GO:1901525 2 / 10 70.5× 3.50e-4 7.51e-3 ✓ sig.
Bergmann glial cell differentiation
ABL1, PTPN11
 GO:0060020 2 / 11 64.1× 4.27e-4 8.64e-3 ✓ sig.
negative regulation of glial cell proliferation
NF1, TP53
 GO:0060253 2 / 11 64.1× 4.27e-4 8.64e-3 ✓ 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 1.95e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis 0.222 2 7.59e-7 4.54e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis-noonan syndrome 0.222 2 7.59e-7 4.54e-6 ✓ sig.
Middle aortic syndrome Moyamoya angiopathy 0.051 2 3.18e-5 1.47e-4 ✓ sig.
17q11.2 microduplication syndrome Cervical lymphadenopathy 0.500 1 6.49e-5 2.33e-4 ✓ sig.
17q11.2 microduplication syndrome Watson syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Cervical lymphadenopathy Watson syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
17q11 microdeletion syndrome Cervical lymphadenopathy 0.333 1 1.30e-4 3.93e-4 ✓ sig.
17q11 microdeletion syndrome Watson syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
17q11 microdeletion syndrome 17q11.2 microduplication syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
legius syndrome Neurofibromatosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Neurofibromatosis-noonan syndrome Watson syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
legius syndrome Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Middle aortic syndrome Watson syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Neurofibromatosis Watson syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
17q11.2 microduplication syndrome Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis-noonan syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cervical lymphadenopathy Middle aortic syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
17q11.2 microduplication syndrome Neurofibromatosis 0.200 1 2.60e-4 6.51e-4 ✓ sig.
17q11.2 microduplication syndrome Middle aortic syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
17q11.2 microduplication syndrome Embryonal nuclear cataract 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cervical lymphadenopathy Embryonal nuclear cataract 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Embryonal nuclear cataract Watson syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cafe-au-lait spots legius syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cafe-au-lait spots Watson syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cafe-au-lait spots Cervical lymphadenopathy 0.143 1 3.90e-4 8.66e-4 ✓ sig.
17q11.2 microduplication syndrome Cafe-au-lait spots 0.143 1 3.90e-4 8.66e-4 ✓ sig.
17q11 microdeletion syndrome Neurofibromatosis 0.167 1 5.19e-4 1.06e-3 ✓ sig.
17q11 microdeletion syndrome Middle aortic syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
17q11.2 microduplication syndrome Moyamoya angiopathy 0.027 1 2.34e-3 3.24e-3 ✓ sig.
Cervical lymphadenopathy Moyamoya angiopathy 0.027 1 2.34e-3 3.24e-3 ✓ sig.
Moyamoya angiopathy Watson syndrome 0.027 1 2.34e-3 3.24e-3 ✓ sig.