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 591

5 diseases · 7 shared-gene connections
5 Diseases
4 Unique genes
0.405 Avg. similarity score
Brain stem astrocytic neoplasm Most-connected disease (4 links)
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Disease 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 ⇵
Brain stem astrocytic neoplasm 4 4 4
Optic tract astrocytoma 3 3 2
Retina neoplasm 3 3 2
Retinitis pigmentosa 86 3 3 1
Fibrodysplasia ossificans progressiva 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KIAA1549 4 / 5 Brain stem astrocytic neoplasm, Optic tract astrocytoma, Retina neoplasm, Retinitis pigmentosa 86
BRAF 3 / 5 Brain stem astrocytic neoplasm, Optic tract astrocytoma, Retina neoplasm
ACVR1 2 / 5 Brain stem astrocytic neoplasm, Fibrodysplasia ossificans progressiva
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 ⇵
Thyroid cancer
BRAF, TP53
 KEGG 2 / 37 162× 5.52e-5 1.18e-3 ✓ sig.
Bladder cancer
BRAF, TP53
 KEGG 2 / 41 146× 6.79e-5 1.39e-3 ✓ sig.
Endometrial cancer
BRAF, TP53
 KEGG 2 / 59 102× 1.41e-4 2.50e-3 ✓ sig.
Signaling by BRAF and RAF fusions
KIAA1549, BRAF
 Reactome 2 / 67 89.6× 1.83e-4 3.06e-3 ✓ sig.
Melanoma
BRAF, TP53
 KEGG 2 / 73 82.3× 2.17e-4 3.50e-3 ✓ sig.
Non-small cell lung cancer
BRAF, TP53
 KEGG 2 / 73 82.3× 2.17e-4 3.50e-3 ✓ sig.
Glioma
BRAF, TP53
 KEGG 2 / 76 79.0× 2.35e-4 3.73e-3 ✓ sig.
Pancreatic cancer
BRAF, TP53
 KEGG 2 / 77 78.0× 2.41e-4 3.80e-3 ✓ sig.
Chronic myeloid leukemia
BRAF, TP53
 KEGG 2 / 77 78.0× 2.41e-4 3.80e-3 ✓ sig.
Colorectal cancer
BRAF, TP53
 KEGG 2 / 87 69.0× 3.08e-4 4.60e-3 ✓ sig.
Prostate cancer
BRAF, TP53
 KEGG 2 / 98 61.3× 3.91e-4 5.53e-3 ✓ sig.
Endocrine resistance
BRAF, TP53
 KEGG 2 / 99 60.7× 3.99e-4 5.61e-3 ✓ sig.
Neurotrophin signaling pathway
BRAF, TP53
 KEGG 2 / 120 50.0× 5.86e-4 7.55e-3 ✓ sig.
Regulation of TP53 Expression
TP53
 Reactome 1 / 2 1,501× 6.66e-4 8.31e-3 ✓ sig.
Fluid shear stress and atherosclerosis
ACVR1, TP53
 KEGG 2 / 141 42.6× 8.09e-4 9.63e-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 ⇵
gastrulation
ACVR1, TP53
 GO:0007369 2 / 38 246× 2.41e-5 1.06e-3 ✓ sig.
T cell differentiation in thymus
BRAF, TP53
 GO:0033077 2 / 41 228× 2.81e-5 1.19e-3 ✓ sig.
cellular response to xenobiotic stimulus
BRAF, TP53
 GO:0071466 2 / 65 144× 7.12e-5 2.40e-3 ✓ sig.
transforming growth factor beta receptor signaling pathway
ACVR1, TP53
 GO:0007179 2 / 112 83.4× 2.12e-4 5.30e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
endocardial cushion cell fate commitment
ACVR1
 GO:0061445 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
regulation of thymocyte apoptotic process
TP53
 GO:0070243 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
oligodendrocyte apoptotic process
TP53
 GO:0097252 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
negative regulation of glucose catabolic process to lactate via pyruvate
TP53
 GO:1904024 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
negative regulation of pentose-phosphate shunt
TP53
 GO:1905856 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
positive regulation of determination of dorsal identity
ACVR1
 GO:2000017 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
intrinsic apoptotic signaling pathway in response to hypoxia
TP53
 GO:1990144 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
positive T cell selection
BRAF
 GO:0043368 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Optic tract astrocytoma Retinitis pigmentosa 86 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Optic tract astrocytoma Retina neoplasm 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Retina neoplasm Retinitis pigmentosa 86 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Brain stem astrocytic neoplasm Fibrodysplasia ossificans progressiva 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain stem astrocytic neoplasm Retinitis pigmentosa 86 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain stem astrocytic neoplasm Optic tract astrocytoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Brain stem astrocytic neoplasm Retina neoplasm 0.333 1 1.29e-4 3.27e-4 ✓ sig.