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 622

5 diseases · 7 shared-gene connections
5 Diseases
2 Unique genes
0.405 Avg. similarity score
Congenital keratoglobus Most-connected disease (4 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 ⇵
Congenital keratoglobus 4 4 2
Glaucoma 3, primary congenital, d 3 3 1
Microspherophakia 3 3 1
Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma 3 3 1
Megalocornea 1, x-linked 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LTBP2 4 / 5 Congenital keratoglobus, Glaucoma 3, primary congenital, d, Microspherophakia, Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma
CHRDL1 2 / 5 Congenital keratoglobus, Megalocornea 1, x-linked
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
CHRDL1
 Reactome 1 / 28 214× 4.66e-3 3.48e-2 ✓ sig.
Molecules associated with elastic fibres
LTBP2
 Reactome 1 / 38 158× 6.32e-3 4.25e-2 ✓ sig.
Post-translational protein phosphorylation
CHRDL1
 Reactome 1 / 108 55.6× 1.79e-2 8.04e-2
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
CHRDL1
 Reactome 1 / 125 48.0× 2.07e-2 8.77e-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 ⇵
establishment of protein localization to extracellular region
LTBP2
 GO:0035592 1 / 3 3,115× 3.21e-4 7.04e-3 ✓ sig.
AMPA glutamate receptor clustering
CHRDL1
 GO:0097113 1 / 5 1,869× 5.35e-4 9.88e-3 ✓ sig.
embryonic axis specification
CHRDL1
 GO:0000578 1 / 7 1,335× 7.49e-4 1.23e-2 ✓ sig.
excitatory chemical synaptic transmission
CHRDL1
 GO:0098976 1 / 13 719× 1.39e-3 1.75e-2 ✓ sig.
supramolecular fiber organization
LTBP2
 GO:0097435 1 / 16 584× 1.71e-3 1.96e-2 ✓ sig.
synapse maturation
CHRDL1
 GO:0060074 1 / 16 584× 1.71e-3 1.96e-2 ✓ sig.
eye development
CHRDL1
 GO:0001654 1 / 49 191× 5.24e-3 3.41e-2 ✓ sig.
protein targeting
LTBP2
 GO:0006605 1 / 49 191× 5.24e-3 3.41e-2 ✓ sig.
protein secretion
LTBP2
 GO:0009306 1 / 65 144× 6.94e-3 3.91e-2 ✓ sig.
regulation of synaptic plasticity
CHRDL1
 GO:0048167 1 / 69 135× 7.37e-3 4.03e-2 ✓ sig.
system development
CHRDL1
 GO:0048731 1 / 74 126× 7.90e-3 4.16e-2 ✓ sig.
negative regulation of BMP signaling pathway
CHRDL1
 GO:0030514 1 / 75 125× 8.01e-3 4.17e-2 ✓ sig.
BMP signaling pathway
CHRDL1
 GO:0030509 1 / 88 106× 9.40e-3 4.51e-2 ✓ sig.
ossification
CHRDL1
 GO:0001503 1 / 110 84.9× 1.17e-2 5.02e-2
transforming growth factor beta receptor signaling pathway
LTBP2
 GO:0007179 1 / 112 83.4× 1.20e-2 5.06e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Glaucoma 3, primary congenital, d Microspherophakia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Glaucoma 3, primary congenital, d Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Microspherophakia Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital keratoglobus Microspherophakia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital keratoglobus Glaucoma 3, primary congenital, d 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital keratoglobus Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital keratoglobus Megalocornea 1, x-linked 0.333 1 1.29e-4 3.27e-4 ✓ sig.