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 127

10 diseases · 16 shared-gene connections
10 Diseases
22 Unique genes
0.169 Avg. similarity score
Coronal craniosynostosis Most-connected disease (6 links)
Log in to save this analysis

Save This Analysis

Disease Searched: duane retraction syndrome 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 ⇵
Coronal craniosynostosis 6 6 3
Brachycephaly 5 5 10
Robinow syndrome 5 5 8
Sweeney-cox syndrome 4 4 1
TWIST1-related craniosynostosis 4 4 1
TCF12-related craniosynostosis 3 3 1
Extraskeletal myxoid chondrosarcoma 2 2 5
Binocular vision disease 1 1 1
Omodysplasia 1 1 2
duane retraction syndrome 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TWIST1 5 / 10 Brachycephaly, Coronal craniosynostosis, Robinow syndrome, Sweeney-cox syndrome and 1 more
TCF12 4 / 10 Brachycephaly, Coronal craniosynostosis, Extraskeletal myxoid chondrosarcoma, TCF12-related craniosynostosis
CHN1 2 / 10 duane retraction syndrome 2, Robinow syndrome
FGFR3 2 / 10 Brachycephaly, Coronal craniosynostosis
FZD2 2 / 10 Omodysplasia, Robinow syndrome
RPS23 2 / 10 Binocular vision disease, Brachycephaly
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 ⇵
Disassembly of the destruction complex and recruitment of AXIN to the membrane
FZD2, DVL1, DVL3, LRP5
 Reactome 4 / 30 72.8× 2.24e-7 1.41e-5 ✓ sig.
Wnt signaling pathway
FZD2, DVL1, DVL3, WNT5A, ROR2, LRP5
 KEGG 6 / 174 18.8× 5.22e-7 2.95e-5 ✓ sig.
WNT5:FZD7-mediated leishmania damping
DVL1, DVL3, WNT5A
 Reactome 3 / 12 136× 1.16e-6 5.93e-5 ✓ sig.
WNT5A-dependent internalization of FZD2, FZD5 and ROR2
FZD2, WNT5A, ROR2
 Reactome 3 / 13 126× 1.51e-6 7.48e-5 ✓ sig.
PCP/CE pathway
DVL1, DVL3, WNT5A
 Reactome 3 / 18 91.0× 4.28e-6 1.79e-4 ✓ sig.
Basal cell carcinoma
FZD2, DVL1, DVL3, WNT5A
 KEGG 4 / 63 34.7× 4.68e-6 1.93e-4 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
FZD2, DVL1, DVL3, WNT5A, FGFR3
 KEGG 5 / 144 19.0× 5.16e-6 2.08e-4 ✓ sig.
Breast cancer
FZD2, DVL1, DVL3, WNT5A, LRP5
 KEGG 5 / 148 18.4× 5.91e-6 2.31e-4 ✓ sig.
Gastric cancer
FZD2, DVL1, DVL3, WNT5A, LRP5
 KEGG 5 / 150 18.2× 6.31e-6 2.43e-4 ✓ sig.
mTOR signaling pathway
FZD2, DVL1, DVL3, WNT5A, LRP5
 KEGG 5 / 158 17.3× 8.13e-6 3.01e-4 ✓ sig.
Hepatocellular carcinoma
FZD2, DVL1, DVL3, WNT5A, LRP5
 KEGG 5 / 170 16.1× 1.16e-5 4.01e-4 ✓ sig.
Melanogenesis
FZD2, DVL1, DVL3, WNT5A
 KEGG 4 / 101 21.6× 3.07e-5 8.93e-4 ✓ sig.
Pathways in cancer
FZD2, DVL1, DVL3, WNT5A, FGFR3, LRP5, TFG
 KEGG 7 / 533 7.2× 3.10e-5 9.03e-4 ✓ sig.
WNT mediated activation of DVL
DVL1, DVL3
 Reactome 2 / 9 121× 1.14e-4 2.58e-3 ✓ sig.
Cushing syndrome
FZD2, DVL1, DVL3, WNT5A
 KEGG 4 / 155 14.1× 1.63e-4 3.42e-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 ⇵
Wnt signaling pathway
FZD2, DVL1, DVL3, WNT5A, NXN, ROR2, LRP5
 GO:0016055 7 / 232 25.6× 6.04e-9 1.10e-6 ✓ sig.
non-canonical Wnt signaling pathway
FZD2, DVL1, DVL3, WNT5A
 GO:0035567 4 / 33 103× 5.76e-8 7.67e-6 ✓ sig.
Wnt signaling pathway, planar cell polarity pathway
FZD2, DVL1, DVL3, WNT5A
 GO:0060071 4 / 34 99.9× 6.53e-8 8.54e-6 ✓ sig.
positive regulation of neuron projection arborization
DVL1, DVL3, WNT5A
 GO:0150012 3 / 8 319× 7.90e-8 1.01e-5 ✓ sig.
canonical Wnt signaling pathway
FZD2, DVL1, DVL3, WNT5A, LRP5
 GO:0060070 5 / 105 40.4× 1.24e-7 1.48e-5 ✓ sig.
positive regulation of DNA-templated transcription
FZD2, DVL3, WNT5A, LRP5, TCF12, ZIC1, NR4A3, TAF15
 GO:0045893 8 / 778 8.7× 1.66e-6 1.28e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
DVL1, DVL3, WNT5A, LRP5, POGZ, TCF12, TWIST1, ZIC1, NR4A3
 GO:0045944 9 / 1,208 6.3× 4.41e-6 2.79e-4 ✓ sig.
cochlea morphogenesis
FZD2, DVL1, WNT5A
 GO:0090103 3 / 28 91.0× 4.55e-6 2.86e-4 ✓ sig.
convergent extension involved in organogenesis
DVL1, WNT5A
 GO:0060029 2 / 5 340× 1.32e-5 6.71e-4 ✓ sig.
embryonic digit morphogenesis
WNT5A, LRP5, TWIST1
 GO:0042733 3 / 57 44.7× 3.98e-5 1.56e-3 ✓ sig.
fibroblast growth factor receptor signaling pathway
WNT5A, FGFR3, PTPN11
 GO:0008543 3 / 60 42.5× 4.64e-5 1.76e-3 ✓ sig.
inner ear morphogenesis
WNT5A, ZIC1, NR4A3
 GO:0042472 3 / 65 39.2× 5.90e-5 2.10e-3 ✓ sig.
genitalia development
WNT5A, PTPN11
 GO:0048806 2 / 10 170× 5.92e-5 2.11e-3 ✓ sig.
presynapse assembly
DVL1, WNT5A
 GO:0099054 2 / 14 121× 1.19e-4 3.55e-3 ✓ sig.
regulation of protein localization
DVL1, DVL3, WNT5A
 GO:0032880 3 / 89 28.6× 1.51e-4 4.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Brachycephaly Coronal craniosynostosis 0.273 3 1.97e-10 1.91e-9 ✓ sig.
Sweeney-cox syndrome TWIST1-related craniosynostosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coronal craniosynostosis Sweeney-cox syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Coronal craniosynostosis TCF12-related craniosynostosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Coronal craniosynostosis TWIST1-related craniosynostosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Extraskeletal myxoid chondrosarcoma TCF12-related craniosynostosis 0.167 1 3.25e-4 7.71e-4 ✓ sig.
duane retraction syndrome 2 Robinow syndrome 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Robinow syndrome Sweeney-cox syndrome 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Robinow syndrome TWIST1-related craniosynostosis 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Binocular vision disease Brachycephaly 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Brachycephaly Sweeney-cox syndrome 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Brachycephaly TCF12-related craniosynostosis 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Brachycephaly TWIST1-related craniosynostosis 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Coronal craniosynostosis Extraskeletal myxoid chondrosarcoma 0.125 1 9.74e-4 1.67e-3 ✓ sig.
Omodysplasia Robinow syndrome 0.100 1 1.04e-3 1.74e-3 ✓ sig.
Coronal craniosynostosis Robinow syndrome 0.091 1 1.56e-3 2.38e-3 ✓ sig.