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 342

6 diseases · 10 shared-gene connections
6 Diseases
11 Unique genes
0.208 Avg. similarity score
Vitamin d dependent rickets 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 ⇵
Vitamin d dependent rickets 5 5 7
Hypocalcemic vitamin d-dependent rickets 4 4 3
Rickets 4 4 6
Peptic esophagitis 3 3 1
vitamin D-dependent rickets, type 1A 3 3 1
Pancreatic trypsinogen deficiency 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
CYP27B1 4 / 6 Hypocalcemic vitamin d-dependent rickets, Rickets, Vitamin d dependent rickets, vitamin D-dependent rickets, type 1A
VDR 4 / 6 Hypocalcemic vitamin d-dependent rickets, Peptic esophagitis, Rickets, Vitamin d dependent rickets
CYP2R1 2 / 6 Hypocalcemic vitamin d-dependent rickets, Vitamin d dependent rickets
PRSS1 2 / 6 Pancreatic trypsinogen deficiency, Vitamin d dependent rickets
TRB 2 / 6 Pancreatic trypsinogen deficiency, Vitamin d dependent rickets
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 ⇵
Vitamin D (calciferol) metabolism
CYP27B1, CYP2R1, VDR
 Reactome 3 / 11 298× 9.39e-8 6.20e-6 ✓ sig.
Parathyroid hormone synthesis, secretion and action
CYP27B1, VDR, PTH, PTH1R
 KEGG 4 / 115 38.0× 2.50e-6 1.07e-4 ✓ sig.
Vitamins
CYP27B1, CYP2R1
 Reactome 2 / 6 364× 1.14e-5 3.74e-4 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption
VDR, PTH, PTH1R
 KEGG 3 / 53 61.8× 1.31e-5 4.19e-4 ✓ sig.
Class B/2 (Secretin family receptors)
PTH, PTH1R
 Reactome 2 / 18 121× 1.16e-4 2.52e-3 ✓ sig.
Steroid biosynthesis
CYP27B1, CYP2R1
 KEGG 2 / 20 109× 1.44e-4 3.01e-3 ✓ sig.
G alpha (s) signalling events
PTH, PTH1R, PDE3B
 Reactome 3 / 140 23.4× 2.39e-4 4.50e-3 ✓ sig.
Defective CYP2R1 causes Rickets vitamin D-dependent 1B (VDDR1B)
CYP2R1
 Reactome 1 / 1 1,092× 9.16e-4 1.27e-2 ✓ sig.
Defective CYP27B1 causes Rickets vitamin D-dependent 1A (VDDR1A)
CYP27B1
 Reactome 1 / 1 1,092× 9.16e-4 1.27e-2 ✓ sig.
PDE3B signalling
PDE3B
 Reactome 1 / 1 1,092× 9.16e-4 1.27e-2 ✓ sig.
Metabolic pathways
CYP27B1, CYP2R1, CA1, HADHB, PDE3B, CYP3A4
 KEGG 6 / 1,563 4.2× 1.24e-3 1.59e-2 ✓ sig.
Beta oxidation of myristoyl-CoA to lauroyl-CoA
HADHB
 Reactome 1 / 3 364× 2.75e-3 2.89e-2 ✓ sig.
Beta oxidation of palmitoyl-CoA to myristoyl-CoA
HADHB
 Reactome 1 / 3 364× 2.75e-3 2.89e-2 ✓ sig.
Neuroactive ligand-receptor interaction
PRSS1, PTH, PTH1R
 KEGG 3 / 370 8.9× 3.98e-3 3.77e-2 ✓ sig.
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA
HADHB
 Reactome 1 / 5 218× 4.57e-3 4.13e-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 ⇵
calcitriol biosynthetic process from calciol
CYP27B1, CYP2R1, CYP3A4
 GO:0036378 3 / 5 1,019× 1.52e-9 3.26e-7 ✓ sig.
vitamin D metabolic process
CYP27B1, CYP2R1, CYP3A4
 GO:0042359 3 / 12 425× 3.33e-8 4.80e-6 ✓ sig.
vitamin D biosynthetic process
CYP27B1, CYP2R1
 GO:0042368 2 / 2 1,699× 3.15e-7 3.17e-5 ✓ sig.
vitamin D catabolic process
CYP27B1, CYP3A4
 GO:0042369 2 / 4 849× 1.89e-6 1.37e-4 ✓ sig.
bone mineralization
CYP27B1, PTH, PTH1R
 GO:0030282 3 / 56 91.0× 4.14e-6 2.58e-4 ✓ sig.
positive regulation of vitamin D receptor signaling pathway
CYP27B1, VDR
 GO:0070564 2 / 6 566× 4.72e-6 2.87e-4 ✓ sig.
vitamin metabolic process
CYP27B1, CYP2R1
 GO:0006766 2 / 6 566× 4.72e-6 2.87e-4 ✓ sig.
positive regulation of inositol phosphate biosynthetic process
PTH, PTH1R
 GO:0060732 2 / 7 485× 6.60e-6 3.74e-4 ✓ sig.
intracellular calcium ion homeostasis
VDR, PTH, PTH1R
 GO:0006874 3 / 113 45.1× 3.43e-5 1.35e-3 ✓ sig.
positive regulation of keratinocyte differentiation
CYP27B1, VDR
 GO:0045618 2 / 20 170× 5.95e-5 2.04e-3 ✓ sig.
response to vitamin D
CYP27B1, PTH
 GO:0033280 2 / 21 162× 6.58e-5 2.21e-3 ✓ sig.
skeletal system development
VDR, PTH, PTH1R
 GO:0001501 3 / 151 33.8× 8.14e-5 2.59e-3 ✓ sig.
decidualization
CYP27B1, VDR
 GO:0046697 2 / 25 136× 9.38e-5 2.88e-3 ✓ sig.
bone resorption
PTH, PTH1R
 GO:0045453 2 / 26 131× 1.02e-4 3.06e-3 ✓ sig.
calcium ion homeostasis
CYP27B1, PTH
 GO:0055074 2 / 42 80.9× 2.68e-4 6.20e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hypocalcemic vitamin d-dependent rickets Vitamin d dependent rickets 0.375 3 5.75e-11 6.20e-10 ✓ sig.
Pancreatic trypsinogen deficiency Vitamin d dependent rickets 0.250 2 1.77e-7 1.25e-6 ✓ sig.
Hypocalcemic vitamin d-dependent rickets Rickets 0.250 2 3.80e-7 2.53e-6 ✓ sig.
Rickets Vitamin d dependent rickets 0.167 2 2.65e-6 1.53e-5 ✓ sig.
Hypocalcemic vitamin d-dependent rickets Peptic esophagitis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hypocalcemic vitamin d-dependent rickets vitamin D-dependent rickets, type 1A 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Peptic esophagitis Rickets 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Rickets vitamin D-dependent rickets, type 1A 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Peptic esophagitis Vitamin d dependent rickets 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Vitamin d dependent rickets vitamin D-dependent rickets, type 1A 0.125 1 4.55e-4 9.55e-4 ✓ sig.