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 351

6 diseases · 13 shared-gene connections
6 Diseases
4 Unique genes
0.350 Avg. similarity score
Hypercalcemic tumoral calcinosis Most-connected disease (5 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 ⇵
Hypercalcemic tumoral calcinosis 5 5 3
Hyperphosphatemic tumoral calcinosis 5 5 3
Tumoral calcinosis 5 5 4
Cerebral embolism 4 4 1
Intracranial embolism 4 4 1
tumoral calcinosis, hyperphosphatemic, familial, 1 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KL 5 / 6 Cerebral embolism, Hypercalcemic tumoral calcinosis, Hyperphosphatemic tumoral calcinosis, Intracranial embolism and 1 more
GALNT3 4 / 6 Hypercalcemic tumoral calcinosis, Hyperphosphatemic tumoral calcinosis, Tumoral calcinosis, tumoral calcinosis, hyperphosphatemic, familial, 1
FGF23 3 / 6 Hypercalcemic tumoral calcinosis, Hyperphosphatemic tumoral calcinosis, Tumoral calcinosis
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 ⇵
FGFR1c and Klotho ligand binding and activation
KL, FGF23
 Reactome 2 / 3 2,002× 2.50e-7 1.45e-5 ✓ sig.
FGFR3c ligand binding and activation
FGF23, GALNT3
 Reactome 2 / 13 462× 6.48e-6 2.33e-4 ✓ sig.
Phospholipase C-mediated cascade: FGFR1
KL, FGF23
 Reactome 2 / 16 375× 9.97e-6 3.34e-4 ✓ sig.
Downstream signaling of activated FGFR1
KL, FGF23
 Reactome 2 / 18 334× 1.27e-5 4.10e-4 ✓ sig.
PI-3K cascade:FGFR1
KL, FGF23
 Reactome 2 / 21 286× 1.74e-5 5.34e-4 ✓ sig.
SHC-mediated cascade:FGFR1
KL, FGF23
 Reactome 2 / 21 286× 1.74e-5 5.34e-4 ✓ sig.
FRS-mediated FGFR1 signaling
KL, FGF23
 Reactome 2 / 23 261× 2.10e-5 6.24e-4 ✓ sig.
Negative regulation of FGFR1 signaling
KL, FGF23
 Reactome 2 / 26 231× 2.70e-5 7.62e-4 ✓ sig.
PI3K Cascade
KL, FGF23
 Reactome 2 / 39 154× 6.14e-5 1.51e-3 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
KL, FGF23
 Reactome 2 / 75 80.1× 2.29e-4 4.35e-3 ✓ sig.
PIP3 activates AKT signaling
KL, FGF23
 Reactome 2 / 93 64.6× 3.52e-4 6.09e-3 ✓ sig.
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
KL, FGF23
 Reactome 2 / 103 58.3× 4.32e-4 7.11e-3 ✓ sig.
Parathyroid hormone synthesis, secretion and action
KL, FGF23
 KEGG 2 / 115 52.2× 5.39e-4 8.44e-3 ✓ sig.
RAF/MAP kinase cascade
KL, FGF23
 Reactome 2 / 124 48.4× 6.26e-4 9.51e-3 ✓ sig.
Signaling by activated point mutants of FGFR1
FGF23
 Reactome 1 / 11 273× 3.66e-3 3.54e-2 ✓ 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 ⇵
fibroblast growth factor receptor signaling pathway
KL, FGF23, GALNT3
 GO:0008543 3 / 60 234× 1.26e-7 1.46e-5 ✓ sig.
positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway
KL, FGF23
 GO:0090080 2 / 5 1,869× 3.44e-7 3.40e-5 ✓ sig.
calcium ion homeostasis
KL, FGF23
 GO:0055074 2 / 42 222× 2.95e-5 1.21e-3 ✓ sig.
positive regulation of vitamin D 24-hydroxylase activity
FGF23
 GO:0010980 1 / 1 4,672× 2.14e-4 5.28e-3 ✓ sig.
regulation of phosphate transport
FGF23
 GO:0010966 1 / 2 2,336× 4.28e-4 8.59e-3 ✓ sig.
carbohydrate metabolic process
KL, GALNT3
 GO:0005975 2 / 175 53.4× 5.17e-4 9.77e-3 ✓ sig.
polysaccharide metabolic process
GALNT3
 GO:0005976 1 / 3 1,557× 6.42e-4 1.13e-2 ✓ sig.
vitamin D catabolic process
FGF23
 GO:0042369 1 / 4 1,168× 8.56e-4 1.36e-2 ✓ sig.
response to sodium phosphate
FGF23
 GO:1904383 1 / 9 519× 1.93e-3 2.20e-2 ✓ sig.
norepinephrine biosynthetic process
KL
 GO:0042421 1 / 9 519× 1.93e-3 2.20e-2 ✓ sig.
cellular response to leptin stimulus
FGF23
 GO:0044320 1 / 10 467× 2.14e-3 2.34e-2 ✓ sig.
negative regulation of hormone secretion
FGF23
 GO:0046888 1 / 10 467× 2.14e-3 2.34e-2 ✓ sig.
intracellular phosphate ion homeostasis
FGF23
 GO:0030643 1 / 10 467× 2.14e-3 2.34e-2 ✓ sig.
cellular response to parathyroid hormone stimulus
FGF23
 GO:0071374 1 / 11 425× 2.35e-3 2.48e-2 ✓ sig.
response to fibroblast growth factor
KL
 GO:0071774 1 / 11 425× 2.35e-3 2.48e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hypercalcemic tumoral calcinosis Hyperphosphatemic tumoral calcinosis 0.750 3 1.64e-12 2.04e-11 ✓ sig.
Hypercalcemic tumoral calcinosis Tumoral calcinosis 0.600 3 6.58e-12 7.74e-11 ✓ sig.
Hyperphosphatemic tumoral calcinosis Tumoral calcinosis 0.600 3 6.58e-12 7.74e-11 ✓ sig.
Cerebral embolism Intracranial embolism 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cerebral embolism Hyperphosphatemic tumoral calcinosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral embolism Hypercalcemic tumoral calcinosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hypercalcemic tumoral calcinosis Intracranial embolism 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hypercalcemic tumoral calcinosis tumoral calcinosis, hyperphosphatemic, familial, 1 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hyperphosphatemic tumoral calcinosis Intracranial embolism 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hyperphosphatemic tumoral calcinosis tumoral calcinosis, hyperphosphatemic, familial, 1 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral embolism Tumoral calcinosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Intracranial embolism Tumoral calcinosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Tumoral calcinosis tumoral calcinosis, hyperphosphatemic, familial, 1 0.200 1 2.60e-4 6.40e-4 ✓ sig.