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 111

11 diseases · 22 shared-gene connections
11 Diseases
52 Unique genes
0.209 Avg. similarity score
Penile hypospadia Most-connected disease (7 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 ⇵
Penile hypospadia 7 7 8
Synpolydactyly 6 6 3
Brachydactyly-syndactyly syndrome 5 5 1
Brachymesophalangy 5 5 1
Hemimelia of limb 5 5 2
Zygodactyly 5 5 1
Brachydactyly 3 3 21
Cryptorchidism 3 3 20
Ghosal hematodiaphyseal dysplasia 2 2 1
Imperforate anus 2 2 9
Biotinidase deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HOXD13 8 / 11 Brachydactyly, Brachydactyly-syndactyly syndrome, Brachymesophalangy, Cryptorchidism and 4 more
NIPBL 3 / 11 Brachydactyly, Cryptorchidism, Penile hypospadia
TBXAS1 3 / 11 Ghosal hematodiaphyseal dysplasia, Imperforate anus, Penile hypospadia
BTD 2 / 11 Biotinidase deficiency, Cryptorchidism
CHST11 2 / 11 Brachydactyly, Synpolydactyly
GABRG3 2 / 11 Imperforate anus, Penile hypospadia
LSM1 2 / 11 Cryptorchidism, Penile hypospadia
NOG 2 / 11 Brachydactyly, Hemimelia of limb
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 ⇵
Signaling by BMP
BMPR1B, SMAD4, BMP2, NOG
 Reactome 4 / 28 33.0× 5.92e-6 2.18e-4 ✓ sig.
G alpha (s) signalling events
GNAS, PTHLH, PDE3A, PTH1R, INSL3, RXFP2
 Reactome 6 / 140 9.9× 2.95e-5 8.23e-4 ✓ sig.
TGF-beta signaling pathway
BMPR1B, GDF5, SMAD4, BMP2, NOG
 KEGG 5 / 108 10.7× 9.95e-5 2.24e-3 ✓ sig.
ADORA2B mediated anti-inflammatory cytokines production
GNAS, PTHLH, PTH1R, INSL3, RXFP2
 Reactome 5 / 128 9.0× 2.21e-4 4.24e-3 ✓ sig.
Relaxin receptors
INSL3, RXFP2
 Reactome 2 / 8 57.7× 5.06e-4 8.04e-3 ✓ sig.
Hippo signaling pathway
CTNNB1, BMPR1B, GDF5, SMAD4, BMP2
 KEGG 5 / 157 7.4× 5.67e-4 8.78e-3 ✓ sig.
Molecules associated with elastic fibres
GDF5, BMP2, FBLN1
 Reactome 3 / 38 18.2× 5.80e-4 8.95e-3 ✓ sig.
Apoptotic cleavage of cell adhesion proteins
CTNNB1, CASP3
 Reactome 2 / 11 42.0× 9.86e-4 1.34e-2 ✓ sig.
TGF-beta receptor signaling activates SMADs
SMAD4, CBL
 Reactome 2 / 12 38.5× 1.18e-3 1.53e-2 ✓ sig.
Pathways in cancer
CTNNB1, GNAS, SMAD4, BMP2, AR, BCL2L1, CASP3, CBL
 KEGG 8 / 533 3.5× 1.92e-3 2.20e-2 ✓ sig.
Hormone signaling
BMPR1B, GNAS, SMAD4, PTHLH, PTH1R
 KEGG 5 / 219 5.3× 2.49e-3 2.69e-2 ✓ sig.
Class B/2 (Secretin family receptors)
PTHLH, PTH1R
 Reactome 2 / 18 25.7× 2.69e-3 2.85e-2 ✓ sig.
Activation of SMO
IHH, IQCE
 Reactome 2 / 18 25.7× 2.69e-3 2.85e-2 ✓ sig.
Gastric acid secretion
SLC9A4, GNAS, CHRM3
 KEGG 3 / 76 9.1× 4.31e-3 3.98e-2 ✓ sig.
Defective SLC26A2 causes chondrodysplasias
SLC26A2
 Reactome 1 / 1 231× 4.33e-3 3.98e-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 ⇵
chondrocyte differentiation
CTNNB1, BMPR1B, GDF5, IHH, SLC26A2, BMP2, PTH1R
 GO:0002062 7 / 61 41.2× 3.30e-10 8.35e-8 ✓ sig.
skeletal system development
CTNNB1, HOXD13, IHH, TRPS1, BMP2, NOG, PTHLH, PTH1R
 GO:0001501 8 / 151 19.0× 8.40e-9 1.48e-6 ✓ sig.
embryonic digit morphogenesis
CTNNB1, CHST11, HOXD13, IHH, SMAD4, NOG
 GO:0042733 6 / 57 37.8× 1.12e-8 1.89e-6 ✓ sig.
in utero embryonic development
CTNNB1, CHST11, IHH, SMAD4, BMP2, NOG, PTH1R, AR, BCL2L1
 GO:0001701 9 / 252 12.8× 2.84e-8 4.19e-6 ✓ sig.
cartilage development
BMPR1B, CHST11, GDF5, IHH, BMP2, NOG
 GO:0051216 6 / 89 24.2× 1.68e-7 1.87e-5 ✓ sig.
seminiferous tubule development
SCAPER, SMAD4, AR, ATRX
 GO:0072520 4 / 21 68.5× 3.08e-7 3.12e-5 ✓ sig.
negative regulation of chondrocyte differentiation
CTNNB1, GDF5, IHH, PTHLH
 GO:0032331 4 / 23 62.5× 4.54e-7 4.31e-5 ✓ sig.
developmental growth
CHST11, GNAS, NIPBL, SMAD4
 GO:0048589 4 / 30 47.9× 1.38e-6 1.07e-4 ✓ sig.
face morphogenesis
NIPBL, NOG, ANKRD11, RAB3GAP1
 GO:0060325 4 / 33 43.6× 2.05e-6 1.47e-4 ✓ sig.
cellular response to BMP stimulus
BMPR1B, SMAD4, BMP2, NOG
 GO:0071773 4 / 33 43.6× 2.05e-6 1.47e-4 ✓ sig.
osteoblast differentiation
CTNNB1, BMPR1B, IHH, SMAD4, BMP2, NOG
 GO:0001649 6 / 137 15.7× 2.15e-6 1.52e-4 ✓ sig.
cell-cell signaling
PCSK5, GDF5, IHH, BMP2, PTHLH, AR, INSL3
 GO:0007267 7 / 234 10.8× 3.66e-6 2.34e-4 ✓ sig.
endocardial cushion formation
ROBO1, BMP2, NOG
 GO:0003272 3 / 12 89.8× 4.39e-6 2.70e-4 ✓ sig.
BMP signaling pathway
BMPR1B, GDF5, SMAD4, BMP2, NOG
 GO:0030509 5 / 88 20.4× 4.51e-6 2.76e-4 ✓ sig.
regulation of developmental growth
NIPBL, AR
 GO:0048638 2 / 2 359× 7.59e-6 4.20e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cryptorchidism Penile hypospadia 0.115 3 1.05e-7 7.71e-7 ✓ sig.
Brachydactyly Hemimelia of limb 0.091 2 1.77e-6 1.05e-5 ✓ sig.
Brachydactyly Synpolydactyly 0.087 2 5.31e-6 2.90e-5 ✓ sig.
Imperforate anus Penile hypospadia 0.125 2 8.49e-6 4.47e-5 ✓ sig.
Brachydactyly-syndactyly syndrome Brachymesophalangy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Brachydactyly-syndactyly syndrome Zygodactyly 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Brachymesophalangy Zygodactyly 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Brachydactyly-syndactyly syndrome Hemimelia of limb 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Brachymesophalangy Hemimelia of limb 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Hemimelia of limb Zygodactyly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Brachydactyly-syndactyly syndrome Synpolydactyly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Brachymesophalangy Synpolydactyly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Synpolydactyly Zygodactyly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Brachydactyly Cryptorchidism 0.050 2 3.32e-4 7.73e-4 ✓ sig.
Hemimelia of limb Synpolydactyly 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Penile hypospadia Zygodactyly 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Ghosal hematodiaphyseal dysplasia Penile hypospadia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Brachymesophalangy Penile hypospadia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Brachydactyly-syndactyly syndrome Penile hypospadia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Ghosal hematodiaphyseal dysplasia Imperforate anus 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Biotinidase deficiency Cryptorchidism 0.048 1 1.30e-3 2.04e-3 ✓ sig.
Penile hypospadia Synpolydactyly 0.091 1 1.56e-3 2.36e-3 ✓ sig.