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 440

6 diseases · 14 shared-gene connections
6 Diseases
7 Unique genes
0.350 Avg. similarity score
Ascending aortic dilation Most-connected disease (5 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 ⇵
Ascending aortic dilation 5 5 1
Failure to thrive in infancy 5 5 1
Generalized joint laxity 5 5 1
Pectus excavatum 5 5 1
Congenital finger flexion contractures 4 4 2
Congenital musculoskeletal anomalies 4 4 6

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

Gene ⇵ Member diseases ⇵ Linked diseases
ABL1 6 / 6 Ascending aortic dilation, Congenital finger flexion contractures, Congenital musculoskeletal anomalies, Failure to thrive in infancy and 2 more
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 ⇵
Chronic myeloid leukemia
ABL1, TGFB2
 KEGG 2 / 77 44.6× 8.34e-4 9.87e-3 ✓ sig.
TGF-beta signaling pathway
SKI, TGFB2
 KEGG 2 / 108 31.8× 1.63e-3 1.64e-2 ✓ sig.
Role of ABL in ROBO-SLIT signaling
ABL1
 Reactome 1 / 4 429× 2.33e-3 2.13e-2 ✓ sig.
Cell cycle
ABL1, TGFB2
 KEGG 2 / 158 21.7× 3.46e-3 2.82e-2 ✓ sig.
Signaling by Retinoic Acid
RARG
 Reactome 1 / 21 81.7× 1.22e-2 6.41e-2
Downregulation of SMAD2/3:SMAD4 transcriptional activity
SKI
 Reactome 1 / 22 78.0× 1.28e-2 6.57e-2
MicroRNAs in cancer
ABL1, TGFB2
 KEGG 2 / 311 11.0× 1.29e-2 6.62e-2
Myogenesis
ABL1
 Reactome 1 / 27 63.5× 1.56e-2 7.44e-2
Signaling by BMP
SKI
 Reactome 1 / 28 61.3× 1.62e-2 7.59e-2
RHO GTPases Activate WASPs and WAVEs
ABL1
 Reactome 1 / 36 47.7× 2.08e-2 8.77e-2
Striated Muscle Contraction
TNNI2
 Reactome 1 / 36 47.7× 2.08e-2 8.77e-2
HDR through Single Strand Annealing (SSA)
ABL1
 Reactome 1 / 37 46.4× 2.14e-2 8.91e-2
Molecules associated with elastic fibres
TGFB2
 Reactome 1 / 38 45.2× 2.19e-2 9.03e-2
Cyclin D associated events in G1
ABL1
 Reactome 1 / 44 39.0× 2.54e-2 9.82e-2
Malaria
TGFB2
 KEGG 1 / 50 34.3× 2.88e-2 1.06e-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 ⇵
cardiac muscle cell proliferation
ABL1, FOXC2, SKI, TGFB2
 GO:0060038 4 / 28 381× 1.41e-10 4.15e-8 ✓ sig.
neural tube closure
ABL1, RARG, SKI, TGFB2
 GO:0001843 4 / 85 126× 1.38e-8 2.34e-6 ✓ sig.
negative regulation of cartilage development
RARG, TGFB2
 GO:0061037 2 / 10 534× 5.40e-6 3.36e-4 ✓ sig.
regulation of extracellular matrix organization
ABL1, TGFB2
 GO:1903053 2 / 12 445× 7.92e-6 4.55e-4 ✓ sig.
positive regulation of cell adhesion mediated by integrin
FOXC2, TGFB2
 GO:0033630 2 / 16 334× 1.44e-5 7.22e-4 ✓ sig.
bone morphogenesis
RARG, SKI
 GO:0060349 2 / 32 167× 5.93e-5 2.10e-3 ✓ sig.
face morphogenesis
SKI, TGFB2
 GO:0060325 2 / 33 162× 6.32e-5 2.20e-3 ✓ sig.
positive regulation of cell migration involved in sprouting angiogenesis
ABL1, FOXC2
 GO:0090050 2 / 37 144× 7.96e-5 2.61e-3 ✓ sig.
blood vessel remodeling
FOXC2, TGFB2
 GO:0001974 2 / 42 127× 1.03e-4 3.16e-3 ✓ sig.
positive regulation of apoptotic process
ABL1, RARG, TGFB2
 GO:0043065 3 / 326 24.6× 1.75e-4 4.61e-3 ✓ sig.
embryonic limb morphogenesis
SKI, TGFB2
 GO:0030326 2 / 59 90.5× 2.04e-4 5.16e-3 ✓ sig.
heart morphogenesis
FOXC2, TGFB2
 GO:0003007 2 / 61 87.5× 2.18e-4 5.39e-3 ✓ sig.
collagen fibril organization
FOXC2, TGFB2
 GO:0030199 2 / 65 82.1× 2.47e-4 5.91e-3 ✓ sig.
positive regulation of neuron apoptotic process
ABL1, TGFB2
 GO:0043525 2 / 65 82.1× 2.47e-4 5.91e-3 ✓ sig.
positive regulation of endothelial cell migration
ABL1, FOXC2
 GO:0010595 2 / 66 80.9× 2.55e-4 6.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Ascending aortic dilation Pectus excavatum 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ascending aortic dilation Failure to thrive in infancy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ascending aortic dilation Generalized joint laxity 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Failure to thrive in infancy Pectus excavatum 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Failure to thrive in infancy Generalized joint laxity 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Generalized joint laxity Pectus excavatum 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ascending aortic dilation Congenital finger flexion contractures 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital finger flexion contractures Pectus excavatum 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital finger flexion contractures Failure to thrive in infancy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital finger flexion contractures Generalized joint laxity 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ascending aortic dilation Congenital musculoskeletal anomalies 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Congenital musculoskeletal anomalies Pectus excavatum 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Congenital musculoskeletal anomalies Failure to thrive in infancy 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Congenital musculoskeletal anomalies Generalized joint laxity 0.143 1 3.87e-4 7.33e-4 ✓ sig.