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 82

13 diseases · 31 shared-gene connections
13 Diseases
32 Unique genes
0.257 Avg. similarity score
Rieger syndrome Most-connected disease (8 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 ⇵
Rieger syndrome 8 8 4
Axenfeld anomaly 7 7 2
Axenfeld-rieger syndrome 7 7 6
Aniridia 6 6 9
Anterior segment dysgenesis 6 6 23
Iridogoniodysgenesis 6 6 2
Anterior segment mesenchymal dysgenesis 5 5 14
FOXC1-related anterior segment dysgenesis 5 5 1
Ring dermoid of cornea 4 4 1
anterior segment dysgenesis 4 4 4 1
anterior segment dysgenesis 8 2 2 1
Axonal neuropathy 1 1 1
aniridia 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PITX2 9 / 13 Aniridia, Anterior segment dysgenesis, anterior segment dysgenesis 4, Anterior segment mesenchymal dysgenesis and 5 more
FOXC1 8 / 13 Aniridia, Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis, Axenfeld anomaly and 4 more
COL4A1 4 / 13 Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis, Axenfeld-rieger syndrome, Rieger syndrome
PAX6 4 / 13 Aniridia, Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis, Axenfeld-rieger syndrome
CPAMD8 3 / 13 Anterior segment dysgenesis, anterior segment dysgenesis 8, Anterior segment mesenchymal dysgenesis
FOXD3 3 / 13 Aniridia, Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis
CYP1B1 2 / 13 Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis
ELP4 2 / 13 Aniridia, Anterior segment dysgenesis
FOXE3 2 / 13 Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis
GBF1 2 / 13 Anterior segment dysgenesis, Axonal neuropathy
IFT140 2 / 13 Anterior segment dysgenesis, Axenfeld-rieger syndrome
PITX3 2 / 13 Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis
PTCH1 2 / 13 Anterior segment dysgenesis, Rieger syndrome
PXDN 2 / 13 Anterior segment dysgenesis, Anterior segment mesenchymal dysgenesis
TRIM44 2 / 13 Aniridia, aniridia 3
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 ⇵
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
FOXD3, SOX2
 Reactome 2 / 13 57.7× 5.27e-4 8.28e-3 ✓ sig.
Crosslinking of collagen fibrils
PXDN, COL4A1
 Reactome 2 / 18 41.7× 1.02e-3 1.38e-2 ✓ sig.
Defective CYP1B1 causes Glaucoma
CYP1B1
 Reactome 1 / 1 375× 2.66e-3 2.83e-2 ✓ sig.
Retinoid metabolism disease events
RBP4
 Reactome 1 / 1 375× 2.66e-3 2.83e-2 ✓ sig.
Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD)
MC2R
 Reactome 1 / 2 188× 5.32e-3 4.56e-2 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
PAX6, SOX2, BMP4
 KEGG 3 / 144 7.8× 6.49e-3 5.20e-2
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation
SOX2
 Reactome 1 / 3 125× 7.97e-3 5.96e-2
Ion homeostasis
RYR1, ITPR1
 Reactome 2 / 54 13.9× 9.03e-3 6.45e-2
Hedgehog 'off' state
IFT140, PTCH1
 Reactome 2 / 56 13.4× 9.68e-3 6.73e-2
TFAP2 (AP-2) family regulates transcription of other transcription factors
PITX2
 Reactome 1 / 4 93.8× 1.06e-2 7.12e-2
Long-term depression
RYR1, ITPR1
 KEGG 2 / 60 12.5× 1.11e-2 7.29e-2
Basal cell carcinoma
BMP4, PTCH1
 KEGG 2 / 63 11.9× 1.21e-2 7.70e-2
Cortisol synthesis and secretion
ITPR1, MC2R
 KEGG 2 / 65 11.5× 1.29e-2 7.95e-2
Melanin biosynthesis
TYR
 Reactome 1 / 5 75.1× 1.33e-2 8.07e-2
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
PAX6
 Reactome 1 / 7 53.6× 1.85e-2 9.85e-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 ⇵
camera-type eye development
FOXC1, PAX6, PITX2, WT1, FOXE3, GJA8, ARHGAP35, BMP4
 GO:0043010 8 / 74 63.1× 3.99e-13 1.97e-10 ✓ sig.
eye development
FOXC1, PAX6, SOX2, FOXE3, PXDN, CPAMD8, RBP4
 GO:0001654 7 / 49 83.4× 1.75e-12 7.58e-10 ✓ sig.
anatomical structure morphogenesis
FOXC1, FOXD3, PAX6, PITX2, EYA1, FOXE3, PITX3
 GO:0009653 7 / 160 25.5× 8.31e-9 1.46e-6 ✓ sig.
pituitary gland development
PAX6, PITX2, SOX2, BMP4
 GO:0021983 4 / 30 77.9× 1.88e-7 2.06e-5 ✓ sig.
iris morphogenesis
PAX6, PITX2, FOXE3
 GO:0061072 3 / 9 195× 3.80e-7 3.72e-5 ✓ sig.
positive regulation of DNA-templated transcription
FOXC1, PAX6, PITX2, SOX2, TRIM44, WT1, EYA1, PITX3, BMP4, PTCH1
 GO:0045893 10 / 778 7.5× 4.14e-7 3.98e-5 ✓ sig.
ureteric bud development
FOXC1, WT1, EYA1, BMP4
 GO:0001657 4 / 41 57.0× 6.86e-7 6.11e-5 ✓ sig.
cornea development in camera-type eye
PAX6, FOXE3, KERA
 GO:0061303 3 / 12 146× 9.93e-7 8.25e-5 ✓ sig.
branching involved in ureteric bud morphogenesis
WT1, EYA1, BMP4, PTCH1
 GO:0001658 4 / 45 51.9× 1.00e-6 8.33e-5 ✓ sig.
lens development in camera-type eye
PAX6, FOXE3, PITX3, GJA8
 GO:0002088 4 / 48 48.7× 1.31e-6 1.03e-4 ✓ sig.
animal organ morphogenesis
PAX6, PITX2, EYA1, PITX3, PTCH1
 GO:0009887 5 / 130 22.5× 2.61e-6 1.78e-4 ✓ sig.
trabecular meshwork development
FOXE3, CYP1B1
 GO:0002930 2 / 2 584× 2.84e-6 1.90e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
FOXC1, FOXD3, PAX6, PITX2, SOX2, WT1, EYA1, PITX3, ATOH7, PRDM5, BMP4
 GO:0045944 11 / 1,208 5.3× 2.87e-6 1.92e-4 ✓ sig.
outflow tract morphogenesis
PITX2, EYA1, RYR1, BMP4
 GO:0003151 4 / 63 37.1× 3.93e-6 2.48e-4 ✓ sig.
blood vessel development
EPHA2, FOXC1, PAX6, BMP4
 GO:0001568 4 / 70 33.4× 6.00e-6 3.47e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Anterior segment dysgenesis Anterior segment mesenchymal dysgenesis 0.357 10 5.55e-27 1.60e-25 ✓ sig.
Anterior segment dysgenesis Axenfeld-rieger syndrome 0.200 5 2.80e-14 4.00e-13 ✓ sig.
Aniridia Anterior segment dysgenesis 0.179 5 5.86e-13 7.63e-12 ✓ sig.
Anterior segment dysgenesis Rieger syndrome 0.167 4 3.78e-12 4.55e-11 ✓ sig.
Anterior segment mesenchymal dysgenesis Axenfeld-rieger syndrome 0.235 4 6.41e-12 7.62e-11 ✓ sig.
Aniridia Anterior segment mesenchymal dysgenesis 0.200 4 5.37e-11 5.83e-10 ✓ sig.
Axenfeld-rieger syndrome Rieger syndrome 0.375 3 1.31e-10 1.37e-9 ✓ sig.
Anterior segment mesenchymal dysgenesis Rieger syndrome 0.188 3 2.39e-9 2.20e-8 ✓ sig.
Aniridia Axenfeld-rieger syndrome 0.231 3 2.76e-9 2.52e-8 ✓ sig.
Axenfeld anomaly Iridogoniodysgenesis 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Iridogoniodysgenesis Rieger syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Axenfeld anomaly Rieger syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Axenfeld-rieger syndrome Iridogoniodysgenesis 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Axenfeld anomaly Axenfeld-rieger syndrome 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Aniridia Axenfeld anomaly 0.200 2 3.04e-7 2.06e-6 ✓ sig.
anterior segment dysgenesis 4 Ring dermoid of cornea 0.500 1 6.49e-5 2.34e-4 ✓ sig.
anterior segment dysgenesis 4 Axenfeld anomaly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Iridogoniodysgenesis Ring dermoid of cornea 0.333 1 1.30e-4 3.90e-4 ✓ sig.
FOXC1-related anterior segment dysgenesis Iridogoniodysgenesis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Axenfeld anomaly Ring dermoid of cornea 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Axenfeld anomaly FOXC1-related anterior segment dysgenesis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
anterior segment dysgenesis 4 Iridogoniodysgenesis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
FOXC1-related anterior segment dysgenesis Rieger syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
anterior segment dysgenesis 4 Rieger syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Rieger syndrome Ring dermoid of cornea 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Axenfeld-rieger syndrome FOXC1-related anterior segment dysgenesis 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Aniridia aniridia 3 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Aniridia FOXC1-related anterior segment dysgenesis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
anterior segment dysgenesis 8 Anterior segment mesenchymal dysgenesis 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Anterior segment dysgenesis anterior segment dysgenesis 8 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Anterior segment dysgenesis Axonal neuropathy 0.042 1 1.49e-3 2.29e-3 ✓ sig.