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 26

20 diseases · 68 shared-gene connections
20 Diseases
35 Unique genes
0.312 Avg. similarity score
Cervical lymphadenopathy Most-connected disease (16 links)
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Disease Searched: Mixed germ cell tumor of central nervous system 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 ⇵
Cervical lymphadenopathy 16 16 1
Watson syndrome 16 16 1
Malignant peripheral nerve sheat tumor 15 15 1
Ganglioneuroma 12 12 1
Familial spinal neurofibromatosis 10 10 1
Cafe-au-lait spots 6 6 6
Glomus tumor 6 6 4
Middle aortic syndrome 6 6 4
Neurofibromatosis 6 6 4
17q11 microdeletion syndrome 5 5 2
Embryonal nuclear cataract 5 5 6
Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal 5 5 1
Mixed germ cell tumor of central nervous system 5 5 2
Neurofibromatosis type 1 5 5 1
Neurofibromatosis-noonan syndrome 5 5 4
Teratoma with malignant transformation 5 5 5
Legius syndrome 3 3 1
Small intestinal enteropathy-associated t-cell lymphoma 3 3 11
Collecting duct carcinoma 1 1 2
Moyamoya disease 2, susceptibility to 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NF1 17 / 20 17q11 microdeletion syndrome, Cafe-au-lait spots, Cervical lymphadenopathy, Embryonal nuclear cataract and 13 more
SPRED1 4 / 20 Cafe-au-lait spots, Legius syndrome, Neurofibromatosis, Neurofibromatosis-noonan syndrome
TP53 3 / 20 Collecting duct carcinoma, Embryonal nuclear cataract, Teratoma with malignant transformation
DICER1 2 / 20 Embryonal nuclear cataract, Teratoma with malignant transformation
RNF213 2 / 20 Middle aortic syndrome, Moyamoya disease 2, susceptibility to
SMARCB1 2 / 20 Collecting duct carcinoma, Glomus tumor
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, MAP2K2, PTPN11, NRAS, STAT5B, KRAS, BRAF
 KEGG 8 / 77 35.7× 4.03e-11 5.29e-9 ✓ sig.
Endocrine resistance
SOS1, GNAS, TP53, JAG1, MAP2K2, NRAS, KRAS, BRAF
 KEGG 8 / 99 27.7× 3.13e-10 3.27e-8 ✓ sig.
Non-small cell lung cancer
SOS1, TP53, MAP2K2, NRAS, STAT5B, KRAS, BRAF
 KEGG 7 / 73 32.9× 1.34e-9 1.21e-7 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
NF1, SPRED1, NRAS, KRAS
 Reactome 4 / 7 196× 2.10e-9 1.81e-7 ✓ sig.
Endometrial cancer
SOS1, TP53, MAP2K2, NRAS, KRAS, BRAF
 KEGG 6 / 59 34.9× 1.57e-8 1.11e-6 ✓ sig.
Downstream signal transduction
SOS1, PTPN11, NRAS, STAT5B, KRAS
 Reactome 5 / 29 59.2× 1.76e-8 1.22e-6 ✓ sig.
Acute myeloid leukemia
SOS1, MAP2K2, NRAS, STAT5B, KRAS, BRAF
 KEGG 6 / 68 30.3× 3.75e-8 2.37e-6 ✓ sig.
Neurotrophin signaling pathway
SOS1, TP53, MAP2K2, PTPN11, NRAS, KRAS, BRAF
 KEGG 7 / 120 20.0× 4.45e-8 2.75e-6 ✓ sig.
Renal cell carcinoma
SOS1, MAP2K2, PTPN11, NRAS, KRAS, BRAF
 KEGG 6 / 70 29.4× 4.48e-8 2.76e-6 ✓ sig.
Growth hormone synthesis, secretion and action
SOS1, GNAS, CACNA1S, MAP2K2, NRAS, STAT5B, KRAS
 KEGG 7 / 122 19.7× 4.99e-8 3.03e-6 ✓ sig.
Thyroid cancer
TP53, MAP2K2, NRAS, KRAS, BRAF
 KEGG 5 / 37 46.4× 6.36e-8 3.77e-6 ✓ sig.
Signaling by SCF-KIT
SOS1, PTPN11, NRAS, STAT5B, KRAS
 Reactome 5 / 37 46.4× 6.36e-8 3.77e-6 ✓ sig.
Glioma
SOS1, TP53, MAP2K2, NRAS, KRAS, BRAF
 KEGG 6 / 76 27.1× 7.37e-8 4.27e-6 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
NF1, SOS1, MAP2K2, NRAS, KRAS, BRAF
 KEGG 6 / 80 25.7× 1.00e-7 5.61e-6 ✓ sig.
Bladder cancer
TP53, MAP2K2, NRAS, KRAS, BRAF
 KEGG 5 / 41 41.8× 1.08e-7 6.01e-6 ✓ 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, NF2, STAT5B, BRAF, BIRC6
 GO:0042127 8 / 201 21.3× 2.86e-9 5.84e-7 ✓ sig.
MAPK cascade
NF1, NF2, MAP2K2, NRAS, KRAS, BRAF
 GO:0000165 6 / 147 21.8× 2.88e-7 3.07e-5 ✓ sig.
negative regulation of Schwann cell proliferation
NF1, DICER1, NF2
 GO:0010626 3 / 8 200× 3.35e-7 3.49e-5 ✓ sig.
Ras protein signal transduction
NF1, SOS1, TP53, NRAS, KRAS
 GO:0007265 5 / 79 33.8× 3.49e-7 3.60e-5 ✓ sig.
glial cell proliferation
NF1, TP53, KRAS
 GO:0014009 3 / 18 89.0× 4.82e-6 3.08e-4 ✓ sig.
Schwann cell development
NF1, SOS1, MAP2K2
 GO:0014044 3 / 20 80.1× 6.71e-6 3.99e-4 ✓ sig.
negative regulation of cell-matrix adhesion
NF1, JAG1, NF2
 GO:0001953 3 / 22 72.8× 9.05e-6 5.03e-4 ✓ sig.
Schwann cell proliferation
NF1, NF2
 GO:0014010 2 / 3 356× 1.02e-5 5.52e-4 ✓ sig.
forebrain astrocyte development
NF1, KRAS
 GO:0021897 2 / 3 356× 1.02e-5 5.52e-4 ✓ sig.
negative regulation of cell migration
NF1, JAG1, NF2, CDH11, SRGAP3
 GO:0030336 5 / 190 14.1× 2.61e-5 1.13e-3 ✓ sig.
negative regulation of non-canonical Wnt signaling pathway
RNF213, ZNRF3
 GO:2000051 2 / 5 214× 3.40e-5 1.38e-3 ✓ sig.
T cell differentiation in thymus
TP53, STAT5B, BRAF
 GO:0033077 3 / 41 39.1× 6.11e-5 2.15e-3 ✓ sig.
regulation of MAPK cascade
NF1, SPRED1, PTPN11
 GO:0043408 3 / 41 39.1× 6.11e-5 2.15e-3 ✓ sig.
multicellular organism growth
SOS1, TP53, PTPN11, COL3A1
 GO:0035264 4 / 115 18.6× 6.15e-5 2.16e-3 ✓ sig.
fibroblast proliferation
NF1, TP53, COL3A1
 GO:0048144 3 / 42 38.1× 6.57e-5 2.26e-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 3.00e-7 1.96e-6 ✓ sig.
Embryonal nuclear cataract Teratoma with malignant transformation 0.250 2 5.00e-7 3.18e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Cafe-au-lait spots Neurofibromatosis-noonan syndrome 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Cervical lymphadenopathy Familial spinal neurofibromatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ganglioneuroma Malignant peripheral nerve sheat tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ganglioneuroma Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial spinal neurofibromatosis Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial spinal neurofibromatosis Ganglioneuroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial spinal neurofibromatosis Malignant peripheral nerve sheat tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial spinal neurofibromatosis Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial spinal neurofibromatosis Neurofibromatosis type 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Neurofibromatosis type 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Neurofibromatosis type 1 Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical lymphadenopathy Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical lymphadenopathy Ganglioneuroma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical lymphadenopathy Malignant peripheral nerve sheat tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical lymphadenopathy Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal Watson syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis type 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ganglioneuroma Melanoma, desmoplastic neurotrophic (2)neurofibromatosis, familial spinal 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ganglioneuroma Neurofibromatosis type 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ganglioneuroma Glomus tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial spinal neurofibromatosis Glomus tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial spinal neurofibromatosis Mixed germ cell tumor of central nervous system 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cervical lymphadenopathy Mixed germ cell tumor of central nervous system 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mixed germ cell tumor of central nervous system Watson syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Mixed germ cell tumor of central nervous system 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ganglioneuroma Mixed germ cell tumor of central nervous system 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Glomus tumor Watson syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cervical lymphadenopathy Glomus tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Glomus tumor Malignant peripheral nerve sheat tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q11 microdeletion syndrome Watson syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q11 microdeletion syndrome Malignant peripheral nerve sheat tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Collecting duct carcinoma Glomus tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q11 microdeletion syndrome Ganglioneuroma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q11 microdeletion syndrome Familial spinal neurofibromatosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q11 microdeletion syndrome Cervical lymphadenopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ganglioneuroma Teratoma with malignant transformation 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Neurofibromatosis Watson syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Neurofibromatosis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Teratoma with malignant transformation 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Teratoma with malignant transformation Watson syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cervical lymphadenopathy Teratoma with malignant transformation 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Neurofibromatosis-noonan syndrome Watson syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cervical lymphadenopathy Neurofibromatosis-noonan syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Familial spinal neurofibromatosis Middle aortic syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Ganglioneuroma Middle aortic syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Malignant peripheral nerve sheat tumor Middle aortic syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Middle aortic syndrome Watson syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cervical lymphadenopathy Middle aortic syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Legius syndrome Neurofibromatosis-noonan syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Legius syndrome Neurofibromatosis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Middle aortic syndrome Moyamoya disease 2, susceptibility to 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Embryonal nuclear cataract Ganglioneuroma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Cervical lymphadenopathy Embryonal nuclear cataract 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Embryonal nuclear cataract Watson syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Embryonal nuclear cataract Malignant peripheral nerve sheat tumor 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Cafe-au-lait spots Legius syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cafe-au-lait spots Malignant peripheral nerve sheat tumor 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cafe-au-lait spots Watson syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cafe-au-lait spots Cervical lymphadenopathy 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cervical lymphadenopathy Small intestinal enteropathy-associated t-cell lymphoma 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Small intestinal enteropathy-associated t-cell lymphoma Watson syndrome 0.083 1 7.10e-4 1.17e-3 ✓ sig.
Malignant peripheral nerve sheat tumor Small intestinal enteropathy-associated t-cell lymphoma 0.083 1 7.10e-4 1.17e-3 ✓ sig.