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 97

12 diseases · 20 shared-gene connections
12 Diseases
66 Unique genes
0.095 Avg. similarity score
Polycystic liver disease Most-connected disease (9 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 ⇵
Polycystic liver disease 9 9 23
Tubulointerstitial kidney disease 6 6 9
Polycystic kidney disease 5 5 48
Hyperuricemic nephropathy 4 4 5
SEC61A1 deficiency 3 3 1
polycystic liver disease 2 3 3 1
ALG9-associated autosomal dominant polycystic kidney disease 2 2 1
autosomal dominant medullary cystic kidney disease with or without hyperuricemia 2 2 2
polycystic kidney disease 3 with or without polycystic liver disease 2 2 1
polycystic liver disease 1 2 2 1
SEC61B-related polycystic liver disease 1 1 1
tubulointerstitial kidney disease, autosomal dominant, 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SEC61A1 4 / 12 Hyperuricemic nephropathy, Polycystic liver disease, SEC61A1 deficiency, Tubulointerstitial kidney disease
SEC63 4 / 12 Polycystic kidney disease, Polycystic liver disease, polycystic liver disease 2, Tubulointerstitial kidney disease
ALG9 3 / 12 ALG9-associated autosomal dominant polycystic kidney disease, Polycystic kidney disease, Polycystic liver disease
GANAB 3 / 12 Polycystic kidney disease, polycystic kidney disease 3 with or without polycystic liver disease, Polycystic liver disease
HNF1B 3 / 12 Hyperuricemic nephropathy, Polycystic liver disease, Tubulointerstitial kidney disease
PRKCSH 3 / 12 Polycystic kidney disease, Polycystic liver disease, polycystic liver disease 1
UMOD 3 / 12 autosomal dominant medullary cystic kidney disease with or without hyperuricemia, Hyperuricemic nephropathy, Tubulointerstitial kidney disease
ALG8 2 / 12 Polycystic kidney disease, Polycystic liver disease
APOA4 2 / 12 autosomal dominant medullary cystic kidney disease with or without hyperuricemia, Tubulointerstitial kidney disease
DKK3 2 / 12 Polycystic kidney disease, Polycystic liver disease
LRP5 2 / 12 Polycystic kidney disease, Polycystic liver disease
LRP6 2 / 12 Polycystic kidney disease, Polycystic liver disease
MUC1 2 / 12 Tubulointerstitial kidney disease, tubulointerstitial kidney disease, autosomal dominant, 2
ONECUT2 2 / 12 Polycystic kidney disease, Polycystic liver disease
PKD2 2 / 12 Polycystic kidney disease, Polycystic liver disease
PKHD1 2 / 12 Polycystic kidney disease, Polycystic liver disease
REN 2 / 12 Hyperuricemic nephropathy, Tubulointerstitial kidney disease
RUVBL1 2 / 12 Polycystic liver disease, Tubulointerstitial kidney disease
SEC61B 2 / 12 Polycystic liver disease, SEC61B-related polycystic liver disease
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 hormone signaling pathway
SRC, TSC2, MTOR, MYC, PIK3CA, PLCE1, CTNNB1
 KEGG 7 / 122 10.4× 4.45e-6 1.73e-4 ✓ sig.
Maturity onset diabetes of the young
HNF1B, HHEX, HNF4A, ONECUT1
 KEGG 4 / 26 28.0× 1.14e-5 3.73e-4 ✓ sig.
Breast cancer
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 148 8.6× 1.59e-5 4.94e-4 ✓ sig.
Gastric cancer
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 150 8.5× 1.73e-5 5.32e-4 ✓ sig.
Hepatocellular carcinoma
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 170 7.5× 3.88e-5 1.04e-3 ✓ sig.
AMPK signaling pathway
CFTR, TSC2, MTOR, PIK3CA, PPARG, HNF4A
 KEGG 6 / 122 8.9× 5.36e-5 1.35e-3 ✓ sig.
GAB1 signalosome
EGFR, SRC, PIK3CA
 Reactome 3 / 17 32.1× 1.02e-4 2.29e-3 ✓ sig.
ErbB signaling pathway
EGFR, SRC, MTOR, MYC, PIK3CA
 KEGG 5 / 86 10.6× 1.06e-4 2.36e-3 ✓ sig.
Colorectal cancer
EGFR, MTOR, MYC, PIK3CA, CTNNB1
 KEGG 5 / 87 10.5× 1.12e-4 2.46e-3 ✓ sig.
Proteoglycans in cancer
EGFR, SRC, MTOR, MYC, PIK3CA, PLCE1, CTNNB1
 KEGG 7 / 204 6.2× 1.23e-4 2.64e-3 ✓ sig.
N-Glycan biosynthesis
ALG9, ALG5, ALG8, GANAB
 KEGG 4 / 55 13.2× 2.30e-4 4.37e-3 ✓ sig.
Human cytomegalovirus infection
EGFR, SRC, TSC2, MTOR, MYC, PIK3CA, CTNNB1
 KEGG 7 / 226 5.6× 2.31e-4 4.38e-3 ✓ sig.
Hedgehog 'off' state
IFT140, DYNC2H1, IFT88, MKS1
 Reactome 4 / 56 13.0× 2.46e-4 4.60e-3 ✓ sig.
Trafficking of myristoylated proteins to the cilium
CYS1, NPHP3
 Reactome 2 / 5 72.8× 2.94e-4 5.28e-3 ✓ sig.
Calnexin/calreticulin cycle
GANAB, PRKCSH
 Reactome 2 / 5 72.8× 2.94e-4 5.28e-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 ⇵
kidney development
BICC1, PKD1, PKD2, HNF1B, REN, UMOD, DYNC2H1, IFT88, NPHP3, PKHD1, ANKS6, AQP11
 GO:0001822 15 / 146 29.1× 2.26e-18 2.83e-15 ✓ sig.
determination of left/right symmetry
ALG5, BICC1, IFT140, NEK8, PKD2, DYNC2H1, NPHP3, ANKS6, CC2D2A, MKKS, MKS1
 GO:0007368 11 / 83 37.5× 5.89e-15 3.98e-12 ✓ sig.
non-motile cilium assembly
IFT140, DYNC2H1, IFT88, NPHP3, CC2D2A, CEP290, MKKS, MKS1
 GO:1905515 8 / 57 39.7× 2.25e-11 7.53e-9 ✓ sig.
cilium assembly
IFT140, DYNC2H1, DZIP1L, IFT88, NPHP3, PKHD1, CC2D2A, CEP290, MKKS, MKS1, ONECUT2, ONECUT1
 GO:0060271 12 / 237 14.3× 3.53e-11 1.12e-8 ✓ sig.
liver development
PKD1, PKD2, HNF1B, SEC63, PIK3CA, PRKCSH, ONECUT2, ONECUT1
 GO:0001889 8 / 87 26.0× 7.33e-10 1.70e-7 ✓ sig.
heart development
BICC1, IFT140, NEK8, PKD1, PKD2, DYNC2H1, TSC2, ANKS6, CC2D2A, MKKS, CTNNB1
 GO:0007507 11 / 273 11.4× 2.79e-9 5.53e-7 ✓ sig.
Wnt signaling pathway
PKD1, PKD2, NPHP3, LRP5, MYC, DKK3, LRP6, CTNNB1, HHEX
 GO:0016055 9 / 232 11.0× 1.20e-7 1.41e-5 ✓ sig.
metanephric ascending thin limb development
PKD1, PKD2, UMOD
 GO:0072218 3 / 4 212× 1.68e-7 1.87e-5 ✓ sig.
embryonic brain development
IFT140, CC2D2A, MKS1, CTNNB1
 GO:1990403 4 / 20 56.6× 6.59e-7 5.90e-5 ✓ sig.
mesonephric duct development
PKD1, PKD2, HNF1B
 GO:0072177 3 / 6 142× 8.35e-7 7.17e-5 ✓ sig.
cell projection organization
IFT140, DYNC2H1, IFT88, CC2D2A, CEP290, DEUP1, MKS1, MTOR
 GO:0030030 8 / 214 10.6× 8.43e-7 7.21e-5 ✓ sig.
mesonephric tubule development
PKD1, PKD2, HNF1B
 GO:0072164 3 / 7 121× 1.46e-6 1.12e-4 ✓ sig.
post-translational protein targeting to membrane, translocation
SEC61B, SEC61A1, SEC63
 GO:0031204 3 / 8 106× 2.33e-6 1.63e-4 ✓ sig.
epidermal growth factor receptor signaling pathway
EGFR, SRC, PIK3CA, PLCE1, CTNNB1
 GO:0007173 5 / 64 22.1× 3.06e-6 2.03e-4 ✓ sig.
branching morphogenesis of an epithelial tube
PKD1, HNF1B, PKHD1, MKS1
 GO:0048754 4 / 29 39.1× 3.15e-6 2.08e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Polycystic kidney disease Polycystic liver disease 0.180 11 1.03e-22 2.33e-21 ✓ sig.
Hyperuricemic nephropathy Tubulointerstitial kidney disease 0.364 4 2.69e-13 3.62e-12 ✓ sig.
Polycystic liver disease Tubulointerstitial kidney disease 0.138 4 4.74e-10 4.68e-9 ✓ sig.
autosomal dominant medullary cystic kidney disease with or without hyperuricemia Tubulointerstitial kidney disease 0.200 2 3.04e-7 2.06e-6 ✓ sig.
Hyperuricemic nephropathy Polycystic liver disease 0.074 2 2.13e-5 1.06e-4 ✓ sig.
Hyperuricemic nephropathy SEC61A1 deficiency 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Tubulointerstitial kidney disease tubulointerstitial kidney disease, autosomal dominant, 2 0.100 1 5.84e-4 1.14e-3 ✓ sig.
SEC61A1 deficiency Tubulointerstitial kidney disease 0.100 1 5.84e-4 1.14e-3 ✓ sig.
polycystic liver disease 2 Tubulointerstitial kidney disease 0.100 1 5.84e-4 1.14e-3 ✓ sig.
autosomal dominant medullary cystic kidney disease with or without hyperuricemia Hyperuricemic nephropathy 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Polycystic liver disease polycystic liver disease 1 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Polycystic liver disease SEC61B-related polycystic liver disease 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Polycystic liver disease SEC61A1 deficiency 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Polycystic liver disease polycystic liver disease 2 0.042 1 1.49e-3 2.29e-3 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic liver disease 0.042 1 1.49e-3 2.29e-3 ✓ sig.
polycystic kidney disease 3 with or without polycystic liver disease Polycystic liver disease 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Polycystic kidney disease polycystic liver disease 2 0.020 1 3.12e-3 4.09e-3 ✓ sig.
Polycystic kidney disease polycystic liver disease 1 0.020 1 3.12e-3 4.09e-3 ✓ sig.
Polycystic kidney disease polycystic kidney disease 3 with or without polycystic liver disease 0.020 1 3.12e-3 4.09e-3 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic kidney disease 0.020 1 3.12e-3 4.09e-3 ✓ sig.