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 23

20 diseases · 53 shared-gene connections
20 Diseases
83 Unique genes
0.193 Avg. similarity score
Bilateral multicystic dysplastic kidney Most-connected disease (10 links)
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Disease Searched: polycystic liver disease 2 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 ⇵
Bilateral multicystic dysplastic kidney 10 10 1
Giant cell tumor of tendon sheath 9 9 1
Polycystic liver disease 9 9 23
Renal dysplasia 9 9 1
17q12 microdeletion syndrome 8 8 2
Multicystic dysplastic kidney 8 8 1
Hyperuricemic nephropathy 7 7 5
Tubulointerstitial kidney disease 6 6 9
Mayer-rokitansky-kuster-hauser syndrome 5 5 7
Ovarian mucinous adenocarcinoma 5 5 6
Polycystic kidney disease 5 5 48
Renal cysts and diabetes syndrome 5 5 3
Uterine cancer 5 5 4
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

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

Gene ⇵ Member diseases ⇵ Linked diseases
HNF1B 12 / 20 17q12 microdeletion syndrome, Bilateral multicystic dysplastic kidney, Giant cell tumor of tendon sheath, Hyperuricemic nephropathy and 8 more
SEC61A1 4 / 20 Hyperuricemic nephropathy, Polycystic liver disease, SEC61A1 deficiency, Tubulointerstitial kidney disease
SEC63 4 / 20 Polycystic kidney disease, Polycystic liver disease, polycystic liver disease 2, Tubulointerstitial kidney disease
ALG9 3 / 20 ALG9-associated autosomal dominant polycystic kidney disease, Polycystic kidney disease, Polycystic liver disease
GANAB 3 / 20 Polycystic kidney disease, polycystic kidney disease 3 with or without polycystic liver disease, Polycystic liver disease
PRKCSH 3 / 20 Polycystic kidney disease, Polycystic liver disease, polycystic liver disease 1
UMOD 3 / 20 autosomal dominant medullary cystic kidney disease with or without hyperuricemia, Hyperuricemic nephropathy, Tubulointerstitial kidney disease
ALG8 2 / 20 Polycystic kidney disease, Polycystic liver disease
APOA4 2 / 20 autosomal dominant medullary cystic kidney disease with or without hyperuricemia, Tubulointerstitial kidney disease
DKK3 2 / 20 Polycystic kidney disease, Polycystic liver disease
LRP5 2 / 20 Polycystic kidney disease, Polycystic liver disease
LRP6 2 / 20 Polycystic kidney disease, Polycystic liver disease
ONECUT2 2 / 20 Polycystic kidney disease, Polycystic liver disease
PKD2 2 / 20 Polycystic kidney disease, Polycystic liver disease
PKHD1 2 / 20 Polycystic kidney disease, Polycystic liver disease
REN 2 / 20 Hyperuricemic nephropathy, Tubulointerstitial kidney disease
RUVBL1 2 / 20 Polycystic liver disease, Tubulointerstitial kidney disease
SEC61B 2 / 20 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, WNT4, TSC2, MTOR, MYC, PIK3CA, PLCE1, CTNNB1, GATA4
 KEGG 9 / 122 10.7× 1.50e-7 9.99e-6 ✓ sig.
Breast cancer
EGFR, WNT4, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 8 / 148 7.8× 7.95e-6 2.96e-4 ✓ sig.
Gastric cancer
EGFR, WNT4, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 8 / 150 7.7× 8.78e-6 3.20e-4 ✓ sig.
Hepatocellular carcinoma
EGFR, WNT4, LRP5, MTOR, MYC, PIK3CA, LRP6, CTNNB1
 KEGG 8 / 170 6.8× 2.19e-5 6.79e-4 ✓ sig.
Maturity onset diabetes of the young
HNF1B, HHEX, HNF4A, ONECUT1
 KEGG 4 / 26 22.3× 2.82e-5 8.38e-4 ✓ sig.
Proteoglycans in cancer
EGFR, SRC, WNT4, MTOR, MYC, PIK3CA, PLCE1, CTNNB1
 KEGG 8 / 204 5.7× 8.00e-5 1.95e-3 ✓ sig.
Thyroid cancer
PAX8, MYC, PPARG, CTNNB1
 KEGG 4 / 37 15.6× 1.18e-4 2.64e-3 ✓ sig.
AMPK signaling pathway
CFTR, TSC2, MTOR, PIK3CA, PPARG, HNF4A
 KEGG 6 / 122 7.1× 1.94e-4 3.92e-3 ✓ sig.
GAB1 signalosome
EGFR, SRC, PIK3CA
 Reactome 3 / 17 25.5× 2.02e-4 4.05e-3 ✓ sig.
ErbB signaling pathway
EGFR, SRC, MTOR, MYC, PIK3CA
 KEGG 5 / 86 8.4× 3.14e-4 5.72e-3 ✓ sig.
Colorectal cancer
EGFR, MTOR, MYC, PIK3CA, CTNNB1
 KEGG 5 / 87 8.3× 3.31e-4 5.99e-3 ✓ sig.
Trafficking of myristoylated proteins to the cilium
CYS1, NPHP3
 Reactome 2 / 5 57.9× 4.66e-4 7.84e-3 ✓ sig.
Calnexin/calreticulin cycle
GANAB, PRKCSH
 Reactome 2 / 5 57.9× 4.66e-4 7.84e-3 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
WNT4, INHBB, MYC, PIK3CA, CTNNB1, ONECUT1
 KEGG 6 / 144 6.0× 4.73e-4 7.95e-3 ✓ sig.
N-Glycan biosynthesis
ALG9, ALG5, ALG8, GANAB
 KEGG 4 / 55 10.5× 5.53e-4 8.94e-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
HNF1B, LHX1, BICC1, PKD1, PKD2, REN, UMOD, DYNC2H1, IFT88, NPHP3, PKHD1, GREB1L
 GO:0001822 19 / 146 29.3× 4.60e-23 1.15e-19 ✓ sig.
mesonephric tubule development
HNF1B, LHX1, PKD1, PKD2, WNT4, PAX8
 GO:0072164 6 / 7 193× 4.46e-14 2.63e-11 ✓ sig.
determination of left/right symmetry
ALG5, BICC1, IFT140, NEK8, PKD2, DYNC2H1, NPHP3, ANKS6, CC2D2A, MKKS, MKS1
 GO:0007368 11 / 83 29.8× 8.33e-14 4.63e-11 ✓ sig.
mesonephric duct development
HNF1B, LHX1, PKD1, PKD2, GREB1L
 GO:0072177 5 / 6 188× 9.15e-12 3.38e-9 ✓ sig.
branching involved in ureteric bud morphogenesis
LHX1, PKD2, GREB1L, WNT4, PAX8, MYC, CTNNB1, PAX2
 GO:0001658 8 / 45 40.0× 2.02e-11 6.98e-9 ✓ sig.
pronephros development
HNF1B, LHX1, PAX8, CEP290, PAX2
 GO:0048793 5 / 7 161× 3.19e-11 1.05e-8 ✓ sig.
non-motile cilium assembly
IFT140, DYNC2H1, IFT88, NPHP3, CC2D2A, CEP290, MKKS, MKS1
 GO:1905515 8 / 57 31.6× 1.49e-10 4.15e-8 ✓ sig.
liver development
HNF1B, PKD1, PKD2, SEC63, WNT4, PIK3CA, PRKCSH, ONECUT2, ONECUT1
 GO:0001889 9 / 87 23.3× 1.67e-10 4.62e-8 ✓ sig.
cilium assembly
IFT140, DYNC2H1, DZIP1L, IFT88, NPHP3, PKHD1, CC2D2A, CEP290, MKKS, MKS1, ONECUT2, ONECUT1
 GO:0060271 12 / 237 11.4× 5.74e-10 1.38e-7 ✓ sig.
mesonephros development
LHX1, REN, WNT4, PAX8, PAX2
 GO:0001823 5 / 13 86.6× 1.91e-9 4.01e-7 ✓ sig.
heart development
BICC1, IFT140, NEK8, PKD1, PKD2, DYNC2H1, TSC2, ANKS6, CC2D2A, MKKS, CTNNB1, GATA4
 GO:0007507 12 / 273 9.9× 2.86e-9 5.68e-7 ✓ sig.
anatomical structure morphogenesis
LHX1, PKD1, IGF2BP2, TBX6, PAX8, DKK3, ONECUT2, ONECUT1, GATA4
 GO:0009653 9 / 160 12.7× 3.77e-8 5.36e-6 ✓ sig.
positive regulation of DNA-templated transcription
HNF1B, LHX1, WNT4, TBX6, PAX8, BRD4, CEP290, LRP5, MYC, PPARG, LRP6, CTNNB1
 GO:0045893 17 / 778 4.9× 4.41e-8 6.13e-6 ✓ sig.
Wnt signaling pathway
PKD1, PKD2, NPHP3, WNT4, LRP5, MYC, DKK3, LRP6, CTNNB1, HHEX
 GO:0016055 10 / 232 9.7× 7.89e-8 1.01e-5 ✓ sig.
negative regulation of mesenchymal cell apoptotic process involved in metanephros development
HNF1B, PAX8, PAX2
 GO:1900212 3 / 3 225× 8.45e-8 1.06e-5 ✓ 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.
Hyperuricemic nephropathy Tubulointerstitial kidney disease 0.364 4 2.69e-13 3.42e-12 ✓ sig.
Polycystic liver disease Tubulointerstitial kidney disease 0.138 4 4.74e-10 4.42e-9 ✓ sig.
autosomal dominant medullary cystic kidney disease with or without hyperuricemia Tubulointerstitial kidney disease 0.200 2 3.04e-7 1.95e-6 ✓ sig.
Hyperuricemic nephropathy Polycystic liver disease 0.074 2 2.13e-5 1.01e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Renal dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Giant cell tumor of tendon sheath 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Multicystic dysplastic kidney 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Giant cell tumor of tendon sheath Renal dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Giant cell tumor of tendon sheath Multicystic dysplastic kidney 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Multicystic dysplastic kidney Renal dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
17q12 microdeletion syndrome Giant cell tumor of tendon sheath 0.333 1 1.30e-4 3.93e-4 ✓ sig.
17q12 microdeletion syndrome Multicystic dysplastic kidney 0.333 1 1.30e-4 3.93e-4 ✓ sig.
17q12 microdeletion syndrome Renal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
17q12 microdeletion syndrome Bilateral multicystic dysplastic kidney 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Renal cysts and diabetes syndrome Renal dysplasia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Multicystic dysplastic kidney Renal cysts and diabetes syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Giant cell tumor of tendon sheath Renal cysts and diabetes syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Renal cysts and diabetes syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Uterine cancer 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Renal dysplasia Uterine cancer 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Giant cell tumor of tendon sheath Uterine cancer 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Multicystic dysplastic kidney Uterine cancer 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Hyperuricemic nephropathy Renal dysplasia 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Giant cell tumor of tendon sheath Hyperuricemic nephropathy 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Hyperuricemic nephropathy SEC61A1 deficiency 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Hyperuricemic nephropathy 0.167 1 3.25e-4 7.71e-4 ✓ sig.
17q12 microdeletion syndrome Renal cysts and diabetes syndrome 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Ovarian mucinous adenocarcinoma Renal dysplasia 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Giant cell tumor of tendon sheath Ovarian mucinous adenocarcinoma 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Multicystic dysplastic kidney Ovarian mucinous adenocarcinoma 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Ovarian mucinous adenocarcinoma 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Mayer-rokitansky-kuster-hauser syndrome Multicystic dysplastic kidney 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Giant cell tumor of tendon sheath Mayer-rokitansky-kuster-hauser syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Mayer-rokitansky-kuster-hauser syndrome Renal dysplasia 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Bilateral multicystic dysplastic kidney Mayer-rokitansky-kuster-hauser syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
17q12 microdeletion syndrome Uterine cancer 0.167 1 5.19e-4 1.06e-3 ✓ sig.
polycystic liver disease 2 Tubulointerstitial kidney disease 0.100 1 5.84e-4 1.16e-3 ✓ sig.
SEC61A1 deficiency Tubulointerstitial kidney disease 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Bilateral multicystic dysplastic kidney Tubulointerstitial kidney disease 0.100 1 5.84e-4 1.16e-3 ✓ sig.
autosomal dominant medullary cystic kidney disease with or without hyperuricemia Hyperuricemic nephropathy 0.143 1 6.49e-4 1.24e-3 ✓ sig.
17q12 microdeletion syndrome Ovarian mucinous adenocarcinoma 0.125 1 7.79e-4 1.41e-3 ✓ sig.
17q12 microdeletion syndrome Mayer-rokitansky-kuster-hauser syndrome 0.111 1 9.09e-4 1.58e-3 ✓ sig.
Polycystic liver disease polycystic liver disease 1 0.042 1 1.49e-3 2.31e-3 ✓ sig.
Polycystic liver disease polycystic liver disease 2 0.042 1 1.49e-3 2.31e-3 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic liver disease 0.042 1 1.49e-3 2.31e-3 ✓ sig.
Polycystic liver disease SEC61A1 deficiency 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.
polycystic kidney disease 3 with or without polycystic liver disease Polycystic liver disease 0.042 1 1.49e-3 2.31e-3 ✓ sig.
Polycystic kidney disease polycystic liver disease 1 0.020 1 3.12e-3 4.10e-3 ✓ sig.
Polycystic kidney disease polycystic liver disease 2 0.020 1 3.12e-3 4.10e-3 ✓ sig.
ALG9-associated autosomal dominant polycystic kidney disease Polycystic kidney disease 0.020 1 3.12e-3 4.10e-3 ✓ sig.
Polycystic kidney disease polycystic kidney disease 3 with or without polycystic liver disease 0.020 1 3.12e-3 4.10e-3 ✓ sig.