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 186

10 diseases · 16 shared-gene connections
10 Diseases
47 Unique genes
0.130 Avg. similarity score
Heterotaxy syndrome Most-connected disease (6 links)
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Disease Searched: Primary ciliary dyskinesia 35 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 ⇵
Heterotaxy syndrome 6 6 25
Situs ambiguus 6 6 21
Situs inversus 5 5 21
Visceral heterotaxy 5 5 14
Heterotaxy, visceral, 10, autosomal, with male infertility 3 3 1
Heterotaxy, visceral, 9, autosomal, with male infertility 2 2 1
Left-right axis malformations 2 2 1
Ciliary dyskinesia, primary, 38 1 1 1
Primary ciliary dyskinesia 13 1 1 1
Primary ciliary dyskinesia 35 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CFAP52 4 / 10 Heterotaxy syndrome, Heterotaxy, visceral, 10, autosomal, with male infertility, Situs inversus, Visceral heterotaxy
CFAP53 4 / 10 Heterotaxy syndrome, Situs ambiguus, Situs inversus, Visceral heterotaxy
CIROP 4 / 10 Heterotaxy syndrome, Situs ambiguus, Situs inversus, Visceral heterotaxy
MMP21 4 / 10 Heterotaxy syndrome, Situs ambiguus, Situs inversus, Visceral heterotaxy
NODAL 4 / 10 Heterotaxy syndrome, Situs ambiguus, Situs inversus, Visceral heterotaxy
PKD1L1 4 / 10 Heterotaxy syndrome, Situs ambiguus, Situs inversus, Visceral heterotaxy
ACVR2B 3 / 10 Heterotaxy syndrome, Situs inversus, Visceral heterotaxy
DAND5 3 / 10 Heterotaxy syndrome, Situs ambiguus, Visceral heterotaxy
LEFTY2 3 / 10 Heterotaxy syndrome, Left-right axis malformations, Visceral heterotaxy
MNS1 3 / 10 Heterotaxy syndrome, Heterotaxy, visceral, 9, autosomal, with male infertility, Situs inversus
CERS1 2 / 10 Heterotaxy syndrome, Situs ambiguus
CFAP300 2 / 10 Ciliary dyskinesia, primary, 38, Situs ambiguus
CFAP45 2 / 10 Heterotaxy syndrome, Situs inversus
CFC1 2 / 10 Heterotaxy syndrome, Visceral heterotaxy
CIROZ 2 / 10 Heterotaxy syndrome, Visceral heterotaxy
DAW1 2 / 10 Heterotaxy syndrome, Visceral heterotaxy
DNAAF1 2 / 10 Primary ciliary dyskinesia 13, Situs ambiguus
DNAH5 2 / 10 Situs ambiguus, Situs inversus
DNAH6 2 / 10 Heterotaxy syndrome, Situs ambiguus
DNAH9 2 / 10 Situs ambiguus, Situs inversus
GDF1 2 / 10 Heterotaxy syndrome, Situs ambiguus
ODAD4 2 / 10 Primary ciliary dyskinesia 35, Situs ambiguus
TEX9 2 / 10 Heterotaxy syndrome, Situs inversus
ZIC3 2 / 10 Heterotaxy syndrome, Situs inversus
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 ⇵
Motor proteins
DNAH5, DNAH6, DNAH9, DNAH7, DNAH11
 KEGG 5 / 194 6.6× 9.24e-4 1.07e-2 ✓ sig.
Transcriptional regulation of pluripotent stem cells
FOXP1, ZIC3
 Reactome 2 / 17 30.1× 1.96e-3 1.88e-2 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
ACVR2B, LEFTY2, ZIC3, NODAL
 KEGG 4 / 144 7.1× 2.37e-3 2.16e-2 ✓ sig.
Huntington disease
DNAH5, DNAH6, DNAH9, DNAH7, DNAH11
 KEGG 5 / 308 4.1× 6.82e-3 4.47e-2 ✓ sig.
TGF-beta signaling pathway
ACVR2B, LEFTY2, NODAL
 KEGG 3 / 108 7.1× 8.61e-3 5.18e-2
Amyotrophic lateral sclerosis
DNAH5, DNAH6, DNAH9, DNAH7, DNAH11
 KEGG 5 / 368 3.5× 1.40e-2 6.99e-2
Pathways of neurodegeneration - multiple diseases
DNAH5, DNAH6, DNAH9, DNAH7, DNAH11
 KEGG 5 / 480 2.7× 3.86e-2 1.25e-1
Signaling by Activin
ACVR2B
 Reactome 1 / 11 23.2× 4.22e-2 1.31e-1
Physiological factors
NKX2-5
 Reactome 1 / 12 21.3× 4.60e-2 1.38e-1
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
ZIC3
 Reactome 1 / 13 19.7× 4.97e-2 1.44e-1
YAP1- and WWTR1 (TAZ)-stimulated gene expression
NKX2-5
 Reactome 1 / 14 18.3× 5.34e-2 1.50e-1
Chromatin modifying enzymes
BRWD1
 Reactome 1 / 20 12.8× 7.55e-2 1.84e-1
BBSome-mediated cargo-targeting to cilium
LZTFL1
 Reactome 1 / 23 11.1× 8.63e-2 1.98e-1
Signaling by BMP
ACVR2B
 Reactome 1 / 28 9.1× 1.04e-1 2.21e-1
Cytokine-cytokine receptor interaction
ACVR2B, GDF1, NODAL
 KEGG 3 / 298 2.6× 1.11e-1 2.30e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
determination of left/right symmetry
ACVR2B, CFC1B, DAW1, MMP21, ZIC3, DAND5, CFC1, NODAL, CFAP53, CCDC39, CCDC40, DNAH5
 GO:0007368 15 / 83 71.9× 9.11e-25 2.77e-21 ✓ sig.
epithelial cilium movement involved in determination of left/right asymmetry
CFAP45, CFAP53, CCDC39, CCDC40, DNAAF1, DNAAF11, ODAD4, DNAH11
 GO:0060287 8 / 13 245× 1.09e-18 1.44e-15 ✓ sig.
cilium movement
CFAP53, CCDC39, CCDC40, DNAAF1, DNAAF11, DNAH5, DNAH9, ODAD4, DNAH7, DNAH11
 GO:0003341 10 / 48 82.8× 2.22e-17 2.43e-14 ✓ sig.
flagellated sperm motility
CFAP52, CFAP45, CFAP53, MNS1, CCDC39, CCDC40, DNAAF11, DNAH5, NME7, DNAH11, LZTFL1
 GO:0030317 11 / 142 30.8× 4.54e-14 2.78e-11 ✓ sig.
epithelial cilium movement involved in extracellular fluid movement
DAW1, CCDC39, CCDC40, DNAAF11, DNAH5, NME7, DNAH11
 GO:0003351 7 / 26 107× 2.53e-13 1.34e-10 ✓ sig.
heart development
ACVR2B, CFC1B, DAW1, ZIC3, CFC1, NODAL, CCDC39, DNAH5, ODAD4, ANKS6, DNAH11, NKX2-5
 GO:0007507 12 / 273 17.5× 2.46e-12 1.08e-9 ✓ sig.
cerebrospinal fluid circulation
DAW1, CFAP45, CCDC39, DNAAF11, DNAH9, ODAD4
 GO:0090660 6 / 18 133× 3.30e-12 1.41e-9 ✓ sig.
cilium movement involved in cell motility
CFAP46, DNAH5, DNAH6, DNAH9, DNAH7, DNAH11
 GO:0060294 6 / 27 88.4× 5.17e-11 1.69e-8 ✓ sig.
determination of pancreatic left/right asymmetry
ZIC3, CCDC39, CCDC40, DNAAF1
 GO:0035469 4 / 5 318× 1.75e-10 5.07e-8 ✓ sig.
axonemal dynein complex assembly
DAW1, CCDC39, CCDC40, DNAAF1, DNAAF11
 GO:0070286 5 / 16 124× 3.46e-10 9.27e-8 ✓ sig.
determination of liver left/right asymmetry
ZIC3, CCDC39, CCDC40, DNAAF1
 GO:0071910 4 / 6 265× 5.25e-10 1.34e-7 ✓ sig.
determination of digestive tract left/right asymmetry
ZIC3, CCDC39, CCDC40, DNAAF1
 GO:0071907 4 / 6 265× 5.25e-10 1.34e-7 ✓ sig.
inner dynein arm assembly
CCDC39, CCDC40, DNAAF1, DNAAF11, DNAH7
 GO:0036159 5 / 18 110× 6.76e-10 1.66e-7 ✓ sig.
outer dynein arm assembly
DAW1, DNAAF1, DNAAF11, DNAH5, ODAD4
 GO:0036158 5 / 22 90.4× 2.06e-9 4.36e-7 ✓ sig.
regulation of cilium beat frequency
CCDC39, CCDC40, DNAAF1, DNAH11
 GO:0003356 4 / 8 199× 2.44e-9 5.06e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Heterotaxy syndrome Visceral heterotaxy 0.429 12 1.19e-33 2.53e-32 ✓ sig.
Heterotaxy syndrome Situs inversus 0.306 11 5.08e-27 9.29e-26 ✓ sig.
Heterotaxy syndrome Situs ambiguus 0.237 9 4.21e-21 6.39e-20 ✓ sig.
Situs inversus Visceral heterotaxy 0.241 7 9.37e-18 1.27e-16 ✓ sig.
Situs ambiguus Situs inversus 0.194 7 3.16e-16 4.02e-15 ✓ sig.
Situs ambiguus Visceral heterotaxy 0.200 6 8.45e-15 1.01e-13 ✓ sig.
Heterotaxy, visceral, 10, autosomal, with male infertility Visceral heterotaxy 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Left-right axis malformations Visceral heterotaxy 0.067 1 9.04e-4 1.41e-3 ✓ sig.
Ciliary dyskinesia, primary, 38 Situs ambiguus 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Heterotaxy, visceral, 10, autosomal, with male infertility Situs inversus 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Heterotaxy, visceral, 9, autosomal, with male infertility Situs inversus 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Primary ciliary dyskinesia 13 Situs ambiguus 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Primary ciliary dyskinesia 35 Situs ambiguus 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Heterotaxy syndrome Heterotaxy, visceral, 10, autosomal, with male infertility 0.038 1 1.61e-3 2.26e-3 ✓ sig.
Heterotaxy syndrome Heterotaxy, visceral, 9, autosomal, with male infertility 0.038 1 1.61e-3 2.26e-3 ✓ sig.
Heterotaxy syndrome Left-right axis malformations 0.038 1 1.61e-3 2.26e-3 ✓ sig.