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.

← Back to all clusters

Cluster 59

14 diseases · 39 shared-gene connections
14 Diseases
16 Unique genes
0.317 Avg. similarity score
Congenital idiopathic intestinal pseudoobstruction Most-connected disease (10 links)
Log in to save this analysis

Save This Analysis

Disease Searched: PLD1-related congenital heart 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 ⇵
Congenital idiopathic intestinal pseudoobstruction 10 10 1
Otopalatodigital spectrum disorder 10 10 1
Terminal osseous dysplasia with pigmentary defects 10 10 1
X-linked ehlers-danlos syndrome 8 8 1
X-linked keloid scarring syndrome 8 8 1
Cardiac valvular dysplasia 6 6 6
Congenital short bowel syndrome 5 5 2
Dysgenesis of corpus callosum 5 5 4
Frontometaphyseal dysplasia 5 5 2
Otopalatodigital syndrome 5 5 2
Conductive hearing loss 3 3 5
Juvenile myoclonic epilepsy 1 1 1
PLD1-related congenital heart disease 1 1 1
multiple congenital anomalies-neurodevelopmental syndrome, x-linked 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FLNA 11 / 14 Cardiac valvular dysplasia, Conductive hearing loss, Congenital idiopathic intestinal pseudoobstruction, Congenital short bowel syndrome and 7 more
CILK1 2 / 14 Dysgenesis of corpus callosum, Juvenile myoclonic epilepsy
OTUD5 2 / 14 Dysgenesis of corpus callosum, multiple congenital anomalies-neurodevelopmental syndrome, x-linked
PLD1 2 / 14 Cardiac valvular dysplasia, PLD1-related congenital heart 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 ⇵
GP1b-IX-V activation signalling
FLNA, COL1A2
 Reactome 2 / 12 125× 1.09e-4 2.34e-3 ✓ sig.
Non-integrin membrane-ECM interactions
COL1A2, COL11A2
 Reactome 2 / 24 62.6× 4.51e-4 7.28e-3 ✓ sig.
MET activates PTK2 signaling
COL1A2, COL11A2
 Reactome 2 / 30 50.0× 7.08e-4 1.03e-2 ✓ sig.
Transport of connexons to the plasma membrane
GJB2
 Reactome 1 / 1 751× 1.33e-3 1.67e-2 ✓ sig.
Collagen chain trimerization
COL1A2, COL11A2
 Reactome 2 / 44 34.1× 1.52e-3 1.86e-2 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL1A2, COL11A2
 Reactome 2 / 51 29.4× 2.04e-3 2.31e-2 ✓ sig.
Collagen degradation
COL1A2, COL11A2
 Reactome 2 / 52 28.9× 2.12e-3 2.38e-2 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL1A2, COL11A2
 Reactome 2 / 67 22.4× 3.50e-3 3.41e-2 ✓ sig.
RIG-I-like receptor signaling pathway
OTUD5, MAP3K7
 KEGG 2 / 72 20.9× 4.03e-3 3.77e-2 ✓ sig.
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
ATM, EYA1
 Reactome 2 / 76 19.8× 4.48e-3 4.07e-2 ✓ sig.
Sensing of DNA Double Strand Breaks
ATM
 Reactome 1 / 6 125× 7.97e-3 5.98e-2
Protein digestion and absorption
COL1A2, COL11A2
 KEGG 2 / 103 14.6× 8.08e-3 6.05e-2
NF-kappa B signaling pathway
ATM, MAP3K7
 KEGG 2 / 105 14.3× 8.39e-3 6.19e-2
Platelet Aggregation (Plug Formation)
COL1A2
 Reactome 1 / 8 93.8× 1.06e-2 7.20e-2
OAS antiviral response
FLNA
 Reactome 1 / 9 83.4× 1.19e-2 7.72e-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 ⇵
collagen fibril organization
ADAMTS19, COL1A2, COL11A2
 GO:0030199 3 / 65 53.9× 2.18e-5 9.65e-4 ✓ sig.
signal transduction in response to DNA damage
ATM, MAP3K7
 GO:0042770 2 / 21 111× 1.43e-4 3.96e-3 ✓ sig.
sensory perception of sound
COL11A2, EYA1, GJB2
 GO:0007605 3 / 162 21.6× 3.30e-4 7.22e-3 ✓ sig.
mitotic spindle assembly
FLNA, OFD1
 GO:0090307 2 / 46 50.8× 6.96e-4 1.20e-2 ✓ sig.
response to ionizing radiation
ATM, EYA1
 GO:0010212 2 / 47 49.7× 7.26e-4 1.24e-2 ✓ sig.
cell projection organization
FLNA, CILK1, OFD1
 GO:0030030 3 / 214 16.4× 7.43e-4 1.26e-2 ✓ sig.
otic vesicle morphogenesis
EYA1
 GO:0071600 1 / 1 1,168× 8.56e-4 1.38e-2 ✓ sig.
regulation of membrane repolarization during atrial cardiac muscle cell action potential
FLNA
 GO:1905000 1 / 1 1,168× 8.56e-4 1.38e-2 ✓ sig.
regulation of membrane repolarization during cardiac muscle cell action potential
FLNA
 GO:1905031 1 / 1 1,168× 8.56e-4 1.38e-2 ✓ sig.
protein heterotrimerization
COL1A2
 GO:0070208 1 / 1 1,168× 8.56e-4 1.38e-2 ✓ sig.
cilium assembly
FLNA, CILK1, OFD1
 GO:0060271 3 / 237 14.8× 9.98e-4 1.52e-2 ✓ sig.
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
ATM, MAP3K7
 GO:0031146 2 / 61 38.3× 1.22e-3 1.72e-2 ✓ sig.
purine ribonucleotide biosynthetic process
MTHFD1
 GO:0009152 1 / 2 584× 1.71e-3 2.10e-2 ✓ sig.
10-formyltetrahydrofolate biosynthetic process
MTHFD1
 GO:0009257 1 / 2 584× 1.71e-3 2.10e-2 ✓ sig.
establishment of RNA localization to telomere
ATM
 GO:0097694 1 / 2 584× 1.71e-3 2.10e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
X-linked ehlers-danlos syndrome X-linked keloid scarring syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Otopalatodigital spectrum disorder Terminal osseous dysplasia with pigmentary defects 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Otopalatodigital spectrum disorder X-linked ehlers-danlos syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Otopalatodigital spectrum disorder X-linked keloid scarring syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction X-linked keloid scarring syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction X-linked ehlers-danlos syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Terminal osseous dysplasia with pigmentary defects 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Otopalatodigital spectrum disorder 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Terminal osseous dysplasia with pigmentary defects X-linked keloid scarring syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Terminal osseous dysplasia with pigmentary defects X-linked ehlers-danlos syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Otopalatodigital syndrome Terminal osseous dysplasia with pigmentary defects 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Frontometaphyseal dysplasia X-linked keloid scarring syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Frontometaphyseal dysplasia X-linked ehlers-danlos syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Frontometaphyseal dysplasia Terminal osseous dysplasia with pigmentary defects 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Frontometaphyseal dysplasia Otopalatodigital spectrum disorder 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Frontometaphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Otopalatodigital syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital short bowel syndrome X-linked keloid scarring syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital short bowel syndrome X-linked ehlers-danlos syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital short bowel syndrome Terminal osseous dysplasia with pigmentary defects 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital short bowel syndrome Otopalatodigital spectrum disorder 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Congenital short bowel syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Otopalatodigital syndrome X-linked keloid scarring syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Otopalatodigital syndrome X-linked ehlers-danlos syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Otopalatodigital spectrum disorder Otopalatodigital syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Dysgenesis of corpus callosum Terminal osseous dysplasia with pigmentary defects 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Dysgenesis of corpus callosum multiple congenital anomalies-neurodevelopmental syndrome, x-linked 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Dysgenesis of corpus callosum Juvenile myoclonic epilepsy 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Dysgenesis of corpus callosum Otopalatodigital spectrum disorder 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Congenital idiopathic intestinal pseudoobstruction Dysgenesis of corpus callosum 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Conductive hearing loss Terminal osseous dysplasia with pigmentary defects 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Conductive hearing loss Otopalatodigital spectrum disorder 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Conductive hearing loss Congenital idiopathic intestinal pseudoobstruction 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Cardiac valvular dysplasia Congenital idiopathic intestinal pseudoobstruction 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cardiac valvular dysplasia X-linked keloid scarring syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cardiac valvular dysplasia PLD1-related congenital heart disease 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cardiac valvular dysplasia X-linked ehlers-danlos syndrome 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cardiac valvular dysplasia Terminal osseous dysplasia with pigmentary defects 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Cardiac valvular dysplasia Otopalatodigital spectrum disorder 0.143 1 3.90e-4 8.66e-4 ✓ sig.