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 188

8 diseases · 12 shared-gene connections
8 Diseases
60 Unique genes
0.064 Avg. similarity score
Polycystic kidney disease Most-connected disease (6 links)
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Disease Searched: SEC61B-related polycystic liver 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 kidney disease 6 6 48
Polycystic liver disease 6 6 23
autosomal dominant polycystic kidney disease 3 3 7
ALG9-associated autosomal dominant polycystic kidney disease 2 2 1
polycystic kidney disease 3 with or without polycystic liver disease 2 2 1
polycystic liver disease 1 2 2 1
renal-hepatic-pancreatic dysplasia 2 2 2 1
SEC61B-related polycystic liver disease 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ALG8 3 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease, Polycystic liver disease
ALG9 3 / 8 ALG9-associated autosomal dominant polycystic kidney disease, Polycystic kidney disease, Polycystic liver disease
GANAB 3 / 8 Polycystic kidney disease, polycystic kidney disease 3 with or without polycystic liver disease, Polycystic liver disease
NEK8 3 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease, renal-hepatic-pancreatic dysplasia 2
PKD2 3 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease, Polycystic liver disease
PRKCSH 3 / 8 Polycystic kidney disease, Polycystic liver disease, polycystic liver disease 1
ALG5 2 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease
DKK3 2 / 8 Polycystic kidney disease, Polycystic liver disease
DNAJB11 2 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease
IFT140 2 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease
LRP5 2 / 8 Polycystic kidney disease, Polycystic liver disease
LRP6 2 / 8 Polycystic kidney disease, Polycystic liver disease
ONECUT2 2 / 8 Polycystic kidney disease, Polycystic liver disease
PKD1 2 / 8 autosomal dominant polycystic kidney disease, Polycystic kidney disease
PKHD1 2 / 8 Polycystic kidney disease, Polycystic liver disease
SEC61B 2 / 8 Polycystic liver disease, SEC61B-related polycystic liver disease
SEC63 2 / 8 Polycystic kidney disease, 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 11.5× 2.32e-6 9.61e-5 ✓ sig.
Maturity onset diabetes of the young
HHEX, HNF1B, HNF4A, ONECUT1
 KEGG 4 / 26 30.8× 7.75e-6 2.62e-4 ✓ sig.
Breast cancer
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 148 9.5× 8.37e-6 2.80e-4 ✓ sig.
Gastric cancer
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 150 9.3× 9.14e-6 3.01e-4 ✓ sig.
Hepatocellular carcinoma
EGFR, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 7 / 170 8.2× 2.07e-5 6.00e-4 ✓ sig.
AMPK signaling pathway
CFTR, TSC2, MTOR, PIK3CA, PPARG, HNF4A
 KEGG 6 / 122 9.8× 3.11e-5 8.40e-4 ✓ sig.
Proteoglycans in cancer
EGFR, SRC, MTOR, MYC, PIK3CA, PLCE1, CTNNB1
 KEGG 7 / 204 6.9× 6.63e-5 1.56e-3 ✓ sig.
ErbB signaling pathway
EGFR, SRC, MTOR, MYC, PIK3CA
 KEGG 5 / 86 11.6× 6.71e-5 1.58e-3 ✓ sig.
Colorectal cancer
EGFR, MTOR, MYC, PIK3CA, CTNNB1
 KEGG 5 / 87 11.5× 7.09e-5 1.65e-3 ✓ sig.
GAB1 signalosome
EGFR, SRC, PIK3CA
 Reactome 3 / 17 35.3× 7.67e-5 1.75e-3 ✓ sig.
Human cytomegalovirus infection
EGFR, SRC, TSC2, MTOR, MYC, PIK3CA, CTNNB1
 KEGG 7 / 226 6.2× 1.26e-4 2.62e-3 ✓ sig.
N-Glycan biosynthesis
ALG9, ALG5, ALG8, GANAB
 KEGG 4 / 55 14.6× 1.59e-4 3.17e-3 ✓ sig.
Hedgehog 'off' state
IFT140, DYNC2H1, IFT88, MKS1
 Reactome 4 / 56 14.3× 1.70e-4 3.35e-3 ✓ sig.
Protein processing in endoplasmic reticulum
DNAJB11, GANAB, SEC61B, PRKCSH, SEC63, SEC61A1
 KEGG 6 / 171 7.0× 2.02e-4 3.83e-3 ✓ sig.
Endometrial cancer
EGFR, MYC, PIK3CA, CTNNB1
 KEGG 4 / 59 13.6× 2.09e-4 3.93e-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, DYNC2H1, IFT88, NPHP3, PKHD1, ANKS6, AQP11, CC2D2A, CEP290, CTNNB1
 GO:0001822 13 / 146 27.7× 8.85e-16 6.94e-13 ✓ sig.
determination of left/right symmetry
ALG5, BICC1, IFT140, NEK8, PKD2, DYNC2H1, NPHP3, ANKS6, CC2D2A, MKKS, MKS1
 GO:0007368 11 / 83 41.3× 1.92e-15 1.42e-12 ✓ sig.
non-motile cilium assembly
IFT140, DYNC2H1, IFT88, NPHP3, CC2D2A, CEP290, MKKS, MKS1
 GO:1905515 8 / 57 43.7× 1.02e-11 3.73e-9 ✓ sig.
cilium assembly
IFT140, DYNC2H1, DZIP1L, IFT88, NPHP3, PKHD1, CC2D2A, CEP290, MKKS, MKS1, ONECUT2, ONECUT1
 GO:0060271 12 / 237 15.8× 1.07e-11 3.92e-9 ✓ sig.
liver development
PKD1, PKD2, PIK3CA, PRKCSH, SEC63, ONECUT2, HNF1B, ONECUT1
 GO:0001889 8 / 87 28.6× 3.34e-10 8.53e-8 ✓ sig.
heart development
BICC1, IFT140, NEK8, PKD1, PKD2, DYNC2H1, TSC2, ANKS6, CC2D2A, MKKS, CTNNB1
 GO:0007507 11 / 273 12.5× 9.62e-10 2.16e-7 ✓ sig.
Wnt signaling pathway
PKD1, PKD2, NPHP3, LRP5, MYC, DKK3, LRP6, CTNNB1, HHEX
 GO:0016055 9 / 232 12.1× 5.12e-8 6.83e-6 ✓ sig.
cell projection organization
IFT140, DYNC2H1, IFT88, CC2D2A, CEP290, DEUP1, MKS1, MTOR
 GO:0030030 8 / 214 11.6× 3.98e-7 3.84e-5 ✓ sig.
embryonic brain development
IFT140, CC2D2A, MKS1, CTNNB1
 GO:1990403 4 / 20 62.3× 4.48e-7 4.24e-5 ✓ sig.
mesonephric duct development
PKD1, PKD2, HNF1B
 GO:0072177 3 / 6 156× 6.25e-7 5.62e-5 ✓ sig.
mesonephric tubule development
PKD1, PKD2, HNF1B
 GO:0072164 3 / 7 133× 1.09e-6 8.93e-5 ✓ sig.
post-translational protein targeting to membrane, translocation
SEC61B, SEC63, SEC61A1
 GO:0031204 3 / 8 117× 1.74e-6 1.30e-4 ✓ sig.
epidermal growth factor receptor signaling pathway
EGFR, SRC, PIK3CA, PLCE1, CTNNB1
 GO:0007173 5 / 64 24.3× 1.90e-6 1.40e-4 ✓ sig.
branching morphogenesis of an epithelial tube
PKD1, PKHD1, MKS1, HNF1B
 GO:0048754 4 / 29 43.0× 2.15e-6 1.54e-4 ✓ sig.
pancreas development
ONECUT2, CTNNB1, HNF1B, ONECUT1
 GO:0031016 4 / 30 41.5× 2.47e-6 1.71e-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 2.21e-21 ✓ sig.
autosomal dominant polycystic kidney disease Polycystic kidney disease 0.143 7 1.81e-18 3.18e-17 ✓ sig.
autosomal dominant polycystic kidney disease Polycystic liver disease 0.069 2 4.46e-5 2.03e-4 ✓ sig.
autosomal dominant polycystic kidney disease renal-hepatic-pancreatic dysplasia 2 0.125 1 4.55e-4 9.72e-4 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic liver disease 0.042 1 1.49e-3 2.31e-3 ✓ sig.
polycystic kidney disease 3 with or without polycystic liver disease Polycystic liver disease 0.042 1 1.49e-3 2.31e-3 ✓ sig.
Polycystic liver disease polycystic liver disease 1 0.042 1 1.49e-3 2.31e-3 ✓ sig.
Polycystic liver disease SEC61B-related polycystic liver disease 0.042 1 1.49e-3 2.31e-3 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic kidney disease 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.
Polycystic kidney disease polycystic liver disease 1 0.020 1 3.12e-3 4.09e-3 ✓ sig.
Polycystic kidney disease renal-hepatic-pancreatic dysplasia 2 0.020 1 3.12e-3 4.09e-3 ✓ sig.