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 341

7 diseases · 18 shared-gene connections
7 Diseases
44 Unique genes
0.228 Avg. similarity score
Malignant triton tumor Most-connected disease (6 links)
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Disease Searched: Thyroid gland spindle cell tumor with thymus-like differentiation 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 ⇵
Malignant triton tumor 6 6 5
Pleural solitary fibrous tumor 6 6 6
Plexiform neurofibroma 6 6 6
Thyroid gland spindle cell tumor with thymus-like differentiation 6 6 5
Aneurysmal bone cyst 4 4 9
Pleural sarcomatoid mesothelioma 4 4 24
Spermatogenic failure, x-linked 4 4 8

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

Gene ⇵ Member diseases ⇵ Linked diseases
SSX1 7 / 7 Aneurysmal bone cyst, Malignant triton tumor, Pleural sarcomatoid mesothelioma, Pleural solitary fibrous tumor and 3 more
SS18 6 / 7 Aneurysmal bone cyst, Malignant triton tumor, Pleural sarcomatoid mesothelioma, Pleural solitary fibrous tumor and 2 more
SSX2 6 / 7 Aneurysmal bone cyst, Malignant triton tumor, Pleural sarcomatoid mesothelioma, Pleural solitary fibrous tumor and 2 more
CDKN2A 2 / 7 Pleural sarcomatoid mesothelioma, Plexiform neurofibroma
KRAS 2 / 7 Pleural sarcomatoid mesothelioma, Thyroid gland spindle cell tumor with thymus-like differentiation
TP53 2 / 7 Pleural sarcomatoid mesothelioma, Pleural solitary fibrous 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 ⇵
Non-small cell lung cancer
TP53, CDKN2A, NRAS, EGFR, KRAS, FHIT
 KEGG 6 / 73 22.4× 2.41e-7 1.21e-5 ✓ sig.
Bladder cancer
TP53, CDKN2A, NRAS, EGFR, KRAS
 KEGG 5 / 41 33.3× 3.55e-7 1.69e-5 ✓ sig.
RAS signaling downstream of NF1 loss-of-function variants
NF1, NRAS, KRAS
 Reactome 3 / 7 117× 1.59e-6 6.23e-5 ✓ sig.
EGFR Transactivation by Gastrin
NRAS, EGFR, KRAS
 Reactome 3 / 9 91.0× 3.80e-6 1.30e-4 ✓ sig.
Melanoma
TP53, CDKN2A, NRAS, EGFR, KRAS
 KEGG 5 / 73 18.7× 6.52e-6 2.04e-4 ✓ sig.
Glioma
TP53, CDKN2A, NRAS, EGFR, KRAS
 KEGG 5 / 76 18.0× 7.96e-6 2.41e-4 ✓ sig.
GRB2 events in EGFR signaling
NRAS, EGFR, KRAS
 Reactome 3 / 13 63.0× 1.28e-5 3.57e-4 ✓ sig.
SHC1 events in EGFR signaling
NRAS, EGFR, KRAS
 Reactome 3 / 14 58.5× 1.62e-5 4.37e-4 ✓ sig.
Constitutive Signaling by EGFRvIII
NRAS, EGFR, KRAS
 Reactome 3 / 15 54.6× 2.02e-5 5.27e-4 ✓ sig.
Cellular senescence
TP53, TSC2, CDKN2A, NBN, NRAS, KRAS
 KEGG 6 / 157 10.4× 2.12e-5 5.47e-4 ✓ sig.
Signaling by ERBB2 ECD mutants
NRAS, EGFR, KRAS
 Reactome 3 / 16 51.2× 2.49e-5 6.24e-4 ✓ sig.
Endocrine resistance
TP53, CDKN2A, NRAS, EGFR, KRAS
 KEGG 5 / 99 13.8× 2.89e-5 7.03e-4 ✓ sig.
RAS GTPase cycle mutants
NRAS, KRAS
 Reactome 2 / 3 182× 3.93e-5 9.01e-4 ✓ sig.
PI3K-Akt signaling pathway
TP53, TSC2, COL1A1, NRAS, EGFR, KRAS, YWHAE, CSF1R
 KEGG 8 / 361 6.0× 4.24e-5 9.60e-4 ✓ sig.
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
NRAS, EGFR, KRAS
 Reactome 3 / 19 43.1× 4.27e-5 9.65e-4 ✓ 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 cyclin-dependent protein serine/threonine kinase activity
LATS2, CDKN2A, LATS1
 GO:0045736 3 / 9 142× 1.01e-6 8.68e-5 ✓ sig.
Ras protein signal transduction
NF1, TP53, CDKN2A, NRAS, KRAS
 GO:0007265 5 / 79 26.9× 1.13e-6 9.52e-5 ✓ sig.
MAPK cascade
NF1, NRAS, EGFR, NF2, KRAS, YWHAE
 GO:0000165 6 / 147 17.3× 1.18e-6 9.84e-5 ✓ sig.
glial cell proliferation
NF1, TP53, KRAS
 GO:0014009 3 / 18 70.8× 9.70e-6 5.31e-4 ✓ sig.
positive regulation of hippo signaling
LATS2, YWHAE, LATS1
 GO:0035332 3 / 21 60.7× 1.57e-5 7.72e-4 ✓ sig.
Schwann cell proliferation
NF1, NF2
 GO:0014010 2 / 3 283× 1.62e-5 7.91e-4 ✓ sig.
forebrain astrocyte development
NF1, KRAS
 GO:0021897 2 / 3 283× 1.62e-5 7.91e-4 ✓ sig.
inner cell mass cell fate commitment
LATS2, LATS1
 GO:0001827 2 / 3 283× 1.62e-5 7.91e-4 ✓ sig.
inner cell mass cellular morphogenesis
LATS2, LATS1
 GO:0001828 2 / 3 283× 1.62e-5 7.91e-4 ✓ sig.
negative regulation of cell-matrix adhesion
NF1, CDKN2A, NF2
 GO:0001953 3 / 22 57.9× 1.82e-5 8.61e-4 ✓ sig.
regulation of cell cycle
TP53, TSC2, CDKN2A, NBN, NF2, BAP1
 GO:0051726 6 / 262 9.7× 3.24e-5 1.33e-3 ✓ sig.
cell population proliferation
NF1, TP53, EGFR, KRAS, BAP1, CSF1R
 GO:0008283 6 / 263 9.7× 3.31e-5 1.35e-3 ✓ sig.
hippo signaling
LATS2, YWHAE, LATS1
 GO:0035329 3 / 28 45.5× 3.83e-5 1.51e-3 ✓ sig.
negative regulation of cell population proliferation
NF1, TP53, TSC2, CDKN2A, NF2, BAP1, CSF1R
 GO:0008285 7 / 444 6.7× 7.31e-5 2.45e-3 ✓ sig.
regulation of tissue remodeling
TP53, DDR2
 GO:0034103 2 / 6 142× 8.08e-5 2.64e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pleural sarcomatoid mesothelioma Plexiform neurofibroma 0.160 4 4.57e-11 4.41e-10 ✓ sig.
Malignant triton tumor Thyroid gland spindle cell tumor with thymus-like differentiation 0.429 3 6.46e-11 6.13e-10 ✓ sig.
Pleural solitary fibrous tumor Thyroid gland spindle cell tumor with thymus-like differentiation 0.429 3 6.46e-11 6.13e-10 ✓ sig.
Plexiform neurofibroma Thyroid gland spindle cell tumor with thymus-like differentiation 0.375 3 1.29e-10 1.20e-9 ✓ sig.
Malignant triton tumor Pleural solitary fibrous tumor 0.375 3 1.61e-10 1.48e-9 ✓ sig.
Malignant triton tumor Plexiform neurofibroma 0.333 3 3.23e-10 2.90e-9 ✓ sig.
Pleural solitary fibrous tumor Plexiform neurofibroma 0.333 3 3.23e-10 2.90e-9 ✓ sig.
Aneurysmal bone cyst Thyroid gland spindle cell tumor with thymus-like differentiation 0.273 3 5.43e-10 4.80e-9 ✓ sig.
Aneurysmal bone cyst Malignant triton tumor 0.250 3 1.36e-9 1.16e-8 ✓ sig.
Aneurysmal bone cyst Pleural solitary fibrous tumor 0.250 3 1.36e-9 1.16e-8 ✓ sig.
Aneurysmal bone cyst Plexiform neurofibroma 0.231 3 2.71e-9 2.26e-8 ✓ sig.
Pleural sarcomatoid mesothelioma Thyroid gland spindle cell tumor with thymus-like differentiation 0.125 3 9.94e-9 7.83e-8 ✓ sig.
Malignant triton tumor Pleural sarcomatoid mesothelioma 0.120 3 2.48e-8 1.87e-7 ✓ sig.
Pleural sarcomatoid mesothelioma Pleural solitary fibrous tumor 0.120 3 2.48e-8 1.87e-7 ✓ sig.
Spermatogenic failure, x-linked Thyroid gland spindle cell tumor with thymus-like differentiation 0.083 1 2.06e-3 2.79e-3 ✓ sig.
Malignant triton tumor Spermatogenic failure, x-linked 0.077 1 2.58e-3 3.34e-3 ✓ sig.
Pleural solitary fibrous tumor Spermatogenic failure, x-linked 0.077 1 2.58e-3 3.34e-3 ✓ sig.
Plexiform neurofibroma Spermatogenic failure, x-linked 0.071 1 3.10e-3 3.93e-3 ✓ sig.