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 229

9 diseases · 30 shared-gene connections
9 Diseases
10 Unique genes
0.373 Avg. similarity score
Encephalocraniocutaneous lipomatosis Most-connected disease (8 links)
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Disease Searched: Pineal body neoplasm 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 ⇵
Encephalocraniocutaneous lipomatosis 8 8 2
Hartsfield syndrome 8 8 1
Osteoglophonic dysplasia 8 8 1
Papillary glioneuronal tumor 8 8 1
Hypogonadotropic hypogonadism 2 with or without anosmia 7 7 1
Craniofaciosynostosis 6 6 2
Pineal body neoplasm 5 5 2
Rosette-forming glioneuronal tumor of fourth ventricule 5 5 5
Trigonocephaly 5 5 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
FGFR1 9 / 9 Craniofaciosynostosis, Encephalocraniocutaneous lipomatosis, Hartsfield syndrome, Hypogonadotropic hypogonadism 2 with or without anosmia and 5 more
FREM1 2 / 9 Craniofaciosynostosis, Trigonocephaly
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 ⇵
Melanoma
FGFR1, KRAS, BRAF, TP53, PIK3CA
 KEGG 5 / 73 82.3× 1.78e-9 1.56e-7 ✓ sig.
Prostate cancer
FGFR1, KRAS, BRAF, TP53, PIK3CA
 KEGG 5 / 98 61.3× 7.96e-9 6.03e-7 ✓ sig.
Breast cancer
FGFR1, KRAS, BRAF, TP53, PIK3CA
 KEGG 5 / 148 40.6× 6.37e-8 3.77e-6 ✓ sig.
Endometrial cancer
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 59 81.4× 1.08e-7 5.98e-6 ✓ sig.
Hepatocellular carcinoma
KRAS, SMARCB1, BRAF, TP53, PIK3CA
 KEGG 5 / 170 35.3× 1.28e-7 6.94e-6 ✓ sig.
Central carbon metabolism in cancer
FGFR1, KRAS, TP53, PIK3CA
 KEGG 4 / 71 67.7× 2.29e-7 1.16e-5 ✓ sig.
Non-small cell lung cancer
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 73 65.8× 2.57e-7 1.28e-5 ✓ sig.
Glioma
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 76 63.2× 3.02e-7 1.47e-5 ✓ sig.
Proteoglycans in cancer
FGFR1, KRAS, BRAF, TP53, PIK3CA
 KEGG 5 / 204 29.4× 3.17e-7 1.53e-5 ✓ sig.
Pancreatic cancer
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 77 62.4× 3.19e-7 1.54e-5 ✓ sig.
Chronic myeloid leukemia
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 77 62.4× 3.19e-7 1.54e-5 ✓ sig.
Colorectal cancer
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 87 55.2× 5.22e-7 2.37e-5 ✓ sig.
Endocrine resistance
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 99 48.5× 8.78e-7 3.72e-5 ✓ sig.
Neurotrophin signaling pathway
KRAS, BRAF, TP53, PIK3CA
 KEGG 4 / 120 40.0× 1.90e-6 7.24e-5 ✓ sig.
Signaling by FGFR1 in disease
FGFR1, KRAS, PIK3CA
 Reactome 3 / 33 109× 2.24e-6 8.30e-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 ⇵
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
FGFR1, KRAS, BRAF
 GO:0000165 3 / 147 38.1× 5.50e-5 1.98e-3 ✓ sig.
phosphatidylinositol-mediated signaling
FGFR1, PIK3CA
 GO:0048015 2 / 24 156× 7.07e-5 2.39e-3 ✓ sig.
negative regulation of neuron apoptotic process
KRAS, BRAF, PIK3CA
 GO:0043524 3 / 160 35.0× 7.07e-5 2.39e-3 ✓ sig.
cardiac muscle cell proliferation
FGFR1, KRAS
 GO:0060038 2 / 28 133× 9.67e-5 3.01e-3 ✓ sig.
T cell differentiation in thymus
BRAF, TP53
 GO:0033077 2 / 41 91.2× 2.09e-4 5.24e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
SMARCB1, TP53
 GO:0045815 2 / 41 91.2× 2.09e-4 5.24e-3 ✓ sig.
cell population proliferation
FGFR1, KRAS, TP53
 GO:0008283 3 / 263 21.3× 3.07e-4 6.90e-3 ✓ sig.
visual learning
KRAS, BRAF
 GO:0008542 2 / 54 69.2× 3.63e-4 7.69e-3 ✓ sig.
stem cell proliferation
FGFR1, TP53
 GO:0072089 2 / 54 69.2× 3.63e-4 7.69e-3 ✓ sig.
epidermal growth factor receptor signaling pathway
BRAF, PIK3CA
 GO:0007173 2 / 64 58.4× 5.10e-4 9.63e-3 ✓ sig.
cellular response to xenobiotic stimulus
BRAF, TP53
 GO:0071466 2 / 65 57.5× 5.27e-4 9.87e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Craniofaciosynostosis Trigonocephaly 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Hartsfield syndrome Osteoglophonic dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Osteoglophonic dysplasia Papillary glioneuronal tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypogonadotropic hypogonadism 2 with or without anosmia Papillary glioneuronal tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypogonadotropic hypogonadism 2 with or without anosmia Osteoglophonic dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hartsfield syndrome Hypogonadotropic hypogonadism 2 with or without anosmia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hartsfield syndrome Papillary glioneuronal tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Hypogonadotropic hypogonadism 2 with or without anosmia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Papillary glioneuronal tumor 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Hartsfield syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Osteoglophonic dysplasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Craniofaciosynostosis Encephalocraniocutaneous lipomatosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hartsfield syndrome Rosette-forming glioneuronal tumor of fourth ventricule 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Papillary glioneuronal tumor Rosette-forming glioneuronal tumor of fourth ventricule 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteoglophonic dysplasia Rosette-forming glioneuronal tumor of fourth ventricule 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hypogonadotropic hypogonadism 2 with or without anosmia Rosette-forming glioneuronal tumor of fourth ventricule 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Rosette-forming glioneuronal tumor of fourth ventricule 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hypogonadotropic hypogonadism 2 with or without anosmia Pineal body neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Papillary glioneuronal tumor Pineal body neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hartsfield syndrome Pineal body neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Osteoglophonic dysplasia Pineal body neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Pineal body neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Craniofaciosynostosis Hypogonadotropic hypogonadism 2 with or without anosmia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Craniofaciosynostosis Papillary glioneuronal tumor 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Craniofaciosynostosis Hartsfield syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Craniofaciosynostosis Osteoglophonic dysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Encephalocraniocutaneous lipomatosis Trigonocephaly 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Osteoglophonic dysplasia Trigonocephaly 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hartsfield syndrome Trigonocephaly 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Papillary glioneuronal tumor Trigonocephaly 0.200 1 2.58e-4 5.38e-4 ✓ sig.