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 180

8 diseases · 12 shared-gene connections
8 Diseases
192 Unique genes
0.151 Avg. similarity score
Nephrolithiasis 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 ⇵
Nephrolithiasis 5 5 120
Urolithiasis 5 5 69
Hyperuricemia 4 4 64
Bladder calculus 3 3 40
Ureterolithiasis 3 3 10
3-hydroxyisobutyric aciduria 2 2 1
Dalmatian hypouricemia 1 1 1
Osteomalacia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ABCG2 5 / 8 Bladder calculus, Hyperuricemia, Nephrolithiasis, Ureterolithiasis and 1 more
BCAS1 5 / 8 Bladder calculus, Hyperuricemia, Nephrolithiasis, Ureterolithiasis and 1 more
ALPL 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
BCAS3 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
CYP24A1 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
KLK15 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
PDILT 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
RGS14 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
RSPH14 4 / 8 Bladder calculus, Nephrolithiasis, Ureterolithiasis, Urolithiasis
VEGFA 4 / 8 Bladder calculus, Hyperuricemia, Nephrolithiasis, Urolithiasis
ABCC6 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
AP1S3 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
AQP1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
CASR 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
CDK12 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
CLDN14 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
DGKD 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
DGKH 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
GCKR 3 / 8 Hyperuricemia, Nephrolithiasis, Urolithiasis
GIPC1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
GIPR 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
H1-0 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
HIBADH 3 / 8 3-hydroxyisobutyric aciduria, Nephrolithiasis, Urolithiasis
KANSL1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
OVOL1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
PRKAG2 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
PTGER1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
SLC22A2 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
SLC30A10 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
SLC34A1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
STC1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
TFAP2B 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
TFAP2D 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
TNPO1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
TRPV5 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
TRPV6 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
UGT8 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
WDR72 3 / 8 Hyperuricemia, Nephrolithiasis, Urolithiasis
ZFPM1 3 / 8 Bladder calculus, Nephrolithiasis, Urolithiasis
AHR 2 / 8 Bladder calculus, Urolithiasis
ARSJ 2 / 8 Nephrolithiasis, Urolithiasis
CLDN10 2 / 8 Nephrolithiasis, Urolithiasis
EPB41L2 2 / 8 Nephrolithiasis, Urolithiasis
FTO 2 / 8 Nephrolithiasis, Urolithiasis
HBB 2 / 8 Bladder calculus, Urolithiasis
HCRTR2 2 / 8 Hyperuricemia, Urolithiasis
KCNK5 2 / 8 Nephrolithiasis, Urolithiasis
MAP2K4 2 / 8 Nephrolithiasis, Urolithiasis
MEPE 2 / 8 Hyperuricemia, Osteomalacia
MINDY4 2 / 8 Nephrolithiasis, Urolithiasis
MIPOL1 2 / 8 Nephrolithiasis, Urolithiasis
NBPF3 2 / 8 Nephrolithiasis, Urolithiasis
OPRL1 2 / 8 Bladder calculus, Urolithiasis
PKN1 2 / 8 Ureterolithiasis, Urolithiasis
SAYSD1 2 / 8 Nephrolithiasis, Urolithiasis
SHROOM3 2 / 8 Nephrolithiasis, Urolithiasis
SLC17A3 2 / 8 Hyperuricemia, Nephrolithiasis
SLC22A12 2 / 8 Dalmatian hypouricemia, Hyperuricemia
SLC26A1 2 / 8 Nephrolithiasis, Urolithiasis
SNX17 2 / 8 Bladder calculus, Urolithiasis
SPATA31H1 2 / 8 Hyperuricemia, Nephrolithiasis
TMEM171 2 / 8 Hyperuricemia, Nephrolithiasis
UMOD 2 / 8 Hyperuricemia, Nephrolithiasis
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 ⇵
Parathyroid hormone synthesis, secretion and action
CASR, CYP24A1, SLC34A1, TRPV5, GNAS, PLCB1, SLC12A3, BGLAP, SLC34A3
 KEGG 9 / 115 4.9× 9.25e-5 2.11e-3 ✓ sig.
Type II Na+/Pi cotransporters
SLC34A1, SLC34A3
 Reactome 2 / 3 41.7× 7.55e-4 1.10e-2 ✓ sig.
Purine salvage
HPRT1, AMPD3, APRT
 Reactome 3 / 13 14.4× 1.02e-3 1.38e-2 ✓ sig.
Nicotinamide salvaging
SLC5A8, PTGS2, RNLS
 Reactome 3 / 19 9.9× 3.23e-3 3.24e-2 ✓ sig.
Platelet degranulation
VEGFA, CTSW, TGFB1, WDR1, PDGFA, AHSG, FN1
 Reactome 7 / 123 3.6× 3.57e-3 3.48e-2 ✓ sig.
Cation-coupled Chloride cotransporters
SLC12A1, SLC12A3
 Reactome 2 / 7 17.9× 5.06e-3 4.41e-2 ✓ sig.
Virion - Hepatitis viruses
CLDN14, CLDN10, CLDN16, CLDN19
 KEGG 4 / 48 5.2× 7.12e-3 5.53e-2
Gamma-carboxylation of protein precursors
BGLAP, GGCX
 Reactome 2 / 9 13.9× 8.50e-3 6.21e-2
Negative regulation of activity of TFAP2 (AP-2) family transcription factors
TFAP2B, TFAP2D
 Reactome 2 / 9 13.9× 8.50e-3 6.21e-2
Erythrocytes take up oxygen and release carbon dioxide
AQP1, HBB
 Reactome 2 / 9 13.9× 8.50e-3 6.21e-2
Glyoxylate metabolism and glycine degradation
AGXT, GRHPR, HAO1
 Reactome 3 / 28 6.7× 9.82e-3 6.79e-2
TRP channels
TRPV5, TRPV6, TRPM6
 Reactome 3 / 28 6.7× 9.82e-3 6.79e-2
Glyoxylate and dicarboxylate metabolism
AGXT, GRHPR, HAO1
 KEGG 3 / 30 6.3× 1.19e-2 7.61e-2
Vitamin D (calciferol) metabolism
CYP24A1, LRP2
 Reactome 2 / 11 11.4× 1.27e-2 7.89e-2
Cell adhesion molecules
CLDN14, CLDN10, CLDN16, CLDN19, HLA-C, HLA-DQA1, HLA-DRB1
 KEGG 7 / 160 2.7× 1.44e-2 8.50e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
urate metabolic process
ABCG2, SLC22A12, GCKR, SLC2A9, SLC17A3
 GO:0046415 5 / 10 48.7× 2.63e-8 3.94e-6 ✓ sig.
urate transport
ABCG2, SLC22A12, SLC2A9, UMOD, SLC17A3
 GO:0015747 5 / 11 44.2× 4.78e-8 6.53e-6 ✓ sig.
potassium ion homeostasis
KCNQ1, UMOD, ATP6V1B1, SCNN1B, SLC12A1, SLC12A3
 GO:0055075 6 / 21 27.8× 5.19e-8 7.01e-6 ✓ sig.
chloride ion homeostasis
KCNQ1, UMOD, ATP6V1B1, SLC12A1, SLC12A3
 GO:0055064 5 / 13 37.4× 1.31e-7 1.51e-5 ✓ sig.
monoatomic ion transport
SLC22A2, SLC30A10, SLC34A1, TRPV5, TRPV6, SLC22A12, KCNQ1, PKD2, SLC25A26, SLC5A8, ATP6V1B1, CLDN10
 GO:0006811 23 / 667 3.4× 3.91e-7 3.80e-5 ✓ sig.
renal urate salt excretion
ABCG2, SLC22A12, UMOD
 GO:0097744 3 / 3 97.3× 1.07e-6 8.74e-5 ✓ sig.
response to vitamin D
ALPL, CYP24A1, STC1, TGFB1, BGLAP
 GO:0033280 5 / 21 23.2× 1.93e-6 1.40e-4 ✓ sig.
cellular response to cAMP
AHR, AQP1, STC1, KCNQ1, PKD2, FBP1, CPS1
 GO:0071320 7 / 58 11.7× 2.09e-6 1.49e-4 ✓ sig.
intracellular phosphate ion homeostasis
ABCC6, SLC34A1, UMOD, SLC34A3
 GO:0030643 4 / 10 38.9× 2.16e-6 1.53e-4 ✓ sig.
kidney development
OVOL1, SLC34A1, SNX17, TFAP2B, VEGFA, BICC1, LRP2, PKD2, UMOD, REN
 GO:0001822 10 / 146 6.7× 2.74e-6 1.85e-4 ✓ sig.
renal absorption
HBB, KCNQ1, CLDN16, CLDN19
 GO:0070293 4 / 11 35.4× 3.37e-6 2.19e-4 ✓ sig.
phospholipase C-activating G protein-coupled receptor signaling pathway
CASR, DGKD, DGKH, OPRL1, PTGER1, VEGFA, HCRTR2, PLCB1, OXGR1
 GO:0007200 9 / 120 7.3× 4.15e-6 2.58e-4 ✓ sig.
calcium ion homeostasis
ABCC6, ALPL, TRPV5, TRPV6, UMOD, ATP6V1B1
 GO:0055074 6 / 42 13.9× 4.20e-6 2.61e-4 ✓ sig.
transmembrane transport
ABCC6, ABCG2, AQP1, SLC22A2, SLC30A10, TRPV5, TRPV6, SLC22A12, KCNQ1, SLC2A9, SLC5A8, SLC12A1
 GO:0055085 19 / 557 3.3× 5.00e-6 3.00e-4 ✓ sig.
IMP salvage
HPRT1, AMPD3, APRT
 GO:0032264 3 / 5 58.4× 1.05e-5 5.42e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bladder calculus Urolithiasis 0.571 40 6.46e-101 7.74e-99 ✓ sig.
Nephrolithiasis Urolithiasis 0.367 51 1.86e-97 2.09e-95 ✓ sig.
Bladder calculus Nephrolithiasis 0.288 36 3.36e-74 2.66e-72 ✓ sig.
Ureterolithiasis Urolithiasis 0.143 10 1.65e-24 4.13e-23 ✓ sig.
Bladder calculus Ureterolithiasis 0.214 9 2.04e-23 4.82e-22 ✓ sig.
Nephrolithiasis Ureterolithiasis 0.074 9 7.77e-19 1.47e-17 ✓ sig.
Hyperuricemia Nephrolithiasis 0.051 9 1.50e-9 1.42e-8 ✓ sig.
Hyperuricemia Urolithiasis 0.047 6 3.96e-7 2.63e-6 ✓ sig.
Dalmatian hypouricemia Hyperuricemia 0.015 1 4.16e-3 5.23e-3 ✓ sig.
Hyperuricemia Osteomalacia 0.015 1 4.16e-3 5.23e-3 ✓ sig.
3-hydroxyisobutyric aciduria Urolithiasis 0.014 1 4.48e-3 5.60e-3 ✓ sig.
3-hydroxyisobutyric aciduria Nephrolithiasis 0.008 1 7.79e-3 9.07e-3 ✓ sig.