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.

← Back to all clusters

Cluster 107

12 diseases · 43 shared-gene connections
12 Diseases
10 Unique genes
0.448 Avg. similarity score
Penile neoplasms Most-connected disease (11 links)
Log in to save this analysis

Save This Analysis

Disease Searched: Thymoma type a 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 ⇵
Penile neoplasms 11 11 4
Splenic neoplasms 11 11 1
Woolly hair nevus 11 11 1
Folliculitis 10 10 2
Non-neoplastic nevus 10 10 1
Acanthoma 5 5 2
Congenital myopathy with excess of muscle spindles 5 5 1
Phakomatosis pigmentokeratotica 5 5 1
Prolactin-producing pituitary gland adenoma 5 5 4
Prolactin-producing pituitary gland carcinoma 5 5 1
Schimmelpenning syndrome 5 5 2
Thymoma type a 3 3 5

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

Gene ⇵ Member diseases ⇵ Linked diseases
HRAS 12 / 12 Acanthoma, Congenital myopathy with excess of muscle spindles, Folliculitis, Non-neoplastic nevus and 8 more
KRAS 3 / 12 Acanthoma, Penile neoplasms, Schimmelpenning syndrome
PIK3CA 2 / 12 Penile neoplasms, Prolactin-producing pituitary gland adenoma
TP53 2 / 12 Folliculitis, Penile neoplasms
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 ⇵
Endometrial cancer
HRAS, KRAS, PIK3CA, TP53, CDH1
 KEGG 5 / 59 102× 5.95e-10 5.84e-8 ✓ sig.
Melanoma
HRAS, KRAS, PIK3CA, TP53, CDH1
 KEGG 5 / 73 82.3× 1.78e-9 1.56e-7 ✓ sig.
Thyroid cancer
HRAS, KRAS, TP53, CDH1
 KEGG 4 / 37 130× 1.58e-8 1.11e-6 ✓ sig.
Bladder cancer
HRAS, KRAS, TP53, CDH1
 KEGG 4 / 41 117× 2.42e-8 1.62e-6 ✓ sig.
Signaling by FGFR3 fusions in cancer
HRAS, KRAS, PIK3CA
 Reactome 3 / 10 360× 4.97e-8 3.03e-6 ✓ sig.
Gastric cancer
HRAS, KRAS, PIK3CA, TP53, CDH1
 KEGG 5 / 150 40.0× 6.81e-8 3.99e-6 ✓ sig.
Signaling by FGFR4 in disease
HRAS, KRAS, PIK3CA
 Reactome 3 / 11 328× 6.84e-8 3.99e-6 ✓ sig.
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants
HRAS, KRAS, PIK3CA
 Reactome 3 / 12 300× 9.11e-8 5.14e-6 ✓ sig.
Signaling by PDGFRA extracellular domain mutants
HRAS, KRAS, PIK3CA
 Reactome 3 / 12 300× 9.11e-8 5.14e-6 ✓ sig.
Constitutive Signaling by EGFRvIII
HRAS, KRAS, PIK3CA
 Reactome 3 / 15 240× 1.88e-7 9.71e-6 ✓ sig.
Central carbon metabolism in cancer
HRAS, KRAS, PIK3CA, TP53
 KEGG 4 / 71 67.7× 2.29e-7 1.16e-5 ✓ sig.
Signaling by ERBB2 ECD mutants
HRAS, KRAS, PIK3CA
 Reactome 3 / 16 225× 2.31e-7 1.17e-5 ✓ sig.
Non-small cell lung cancer
HRAS, KRAS, PIK3CA, TP53
 KEGG 4 / 73 65.8× 2.57e-7 1.28e-5 ✓ sig.
Glioma
HRAS, KRAS, PIK3CA, TP53
 KEGG 4 / 76 63.2× 3.02e-7 1.47e-5 ✓ sig.
Chronic myeloid leukemia
HRAS, KRAS, PIK3CA, TP53
 KEGG 4 / 77 62.4× 3.19e-7 1.54e-5 ✓ 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 ⇵
Ras protein signal transduction
HRAS, KRAS, TP53
 GO:0007265 3 / 79 71.0× 8.54e-6 4.82e-4 ✓ sig.
neuron apoptotic process
HRAS, KRAS, TP53
 GO:0051402 3 / 98 57.2× 1.63e-5 7.93e-4 ✓ sig.
regulation of long-term neuronal synaptic plasticity
HRAS, KRAS
 GO:0048169 2 / 18 208× 3.93e-5 1.53e-3 ✓ sig.
glial cell proliferation
KRAS, TP53
 GO:0014009 2 / 18 208× 3.93e-5 1.53e-3 ✓ sig.
positive regulation of cellular senescence
KRAS, TP53
 GO:2000774 2 / 20 187× 4.87e-5 1.81e-3 ✓ sig.
MAPK cascade
HRAS, KRAS, MEN1
 GO:0000165 3 / 147 38.1× 5.50e-5 1.98e-3 ✓ sig.
negative regulation of neuron apoptotic process
HRAS, KRAS, PIK3CA
 GO:0043524 3 / 160 35.0× 7.07e-5 2.39e-3 ✓ sig.
response to gamma radiation
TP53, MEN1
 GO:0010332 2 / 27 138× 8.98e-5 2.86e-3 ✓ sig.
cellular response to gamma radiation
HRAS, TP53
 GO:0071480 2 / 28 133× 9.67e-5 3.01e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, MEN1
 GO:0045815 2 / 41 91.2× 2.09e-4 5.24e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
HRAS, TP53, HOXA13, MEN1, GTF2I
 GO:0045944 5 / 1,208 7.7× 2.14e-4 5.32e-3 ✓ sig.
fibroblast proliferation
HRAS, TP53
 GO:0048144 2 / 42 89.0× 2.19e-4 5.41e-3 ✓ sig.
intrinsic apoptotic signaling pathway
HRAS, TP53
 GO:0097193 2 / 45 83.1× 2.52e-4 5.98e-3 ✓ sig.
adipose tissue development
HRAS, PIK3CA
 GO:0060612 2 / 46 81.2× 2.63e-4 6.19e-3 ✓ sig.
response to UV
TP53, MEN1
 GO:0009411 2 / 54 69.2× 3.63e-4 7.69e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Prolactin-producing pituitary gland carcinoma Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Penile neoplasms Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Penile neoplasms Phakomatosis pigmentokeratotica 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Phakomatosis pigmentokeratotica Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Phakomatosis pigmentokeratotica Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Phakomatosis pigmentokeratotica 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Phakomatosis pigmentokeratotica 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Penile neoplasms Prolactin-producing pituitary gland carcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Prolactin-producing pituitary gland carcinoma Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acanthoma Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Prolactin-producing pituitary gland carcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Prolactin-producing pituitary gland carcinoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Penile neoplasms Schimmelpenning syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Schimmelpenning syndrome Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Schimmelpenning syndrome Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Schimmelpenning syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Schimmelpenning syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Splenic neoplasms Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acanthoma Penile neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acanthoma Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acanthoma Folliculitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acanthoma Non-neoplastic nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy with excess of muscle spindles Penile neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy with excess of muscle spindles Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy with excess of muscle spindles Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy with excess of muscle spindles Folliculitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital myopathy with excess of muscle spindles Non-neoplastic nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Penile neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Woolly hair nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Folliculitis Non-neoplastic nevus 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Penile neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Penile neoplasms Splenic neoplasms 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-neoplastic nevus Prolactin-producing pituitary gland adenoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Folliculitis Prolactin-producing pituitary gland adenoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Prolactin-producing pituitary gland adenoma Woolly hair nevus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Prolactin-producing pituitary gland adenoma Splenic neoplasms 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Penile neoplasms Prolactin-producing pituitary gland adenoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Penile neoplasms Thymoma type a 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Splenic neoplasms Thymoma type a 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Thymoma type a Woolly hair nevus 0.167 1 3.23e-4 6.41e-4 ✓ sig.