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 108

11 diseases · 19 shared-gene connections
11 Diseases
43 Unique genes
0.242 Avg. similarity score
11p11.2 deletion syndrome Most-connected disease (6 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 ⇵
11p11.2 deletion syndrome 6 6 3
Potocki-shaffer syndrome 6 6 3
Parietal foramina 5 5 2
Seizures, scoliosis, and macrocephaly/microcephaly syndrome 4 4 1
exostoses, multiple, type 2 4 4 1
Frontonasal dysplasia with alopecia and genital anomaly 3 3 1
Posterior cortical atrophy 3 3 13
Exostoses 2 2 28
Intellectual developmental disorder behavioral dysmorphic 2 2 1
craniosynostosis 2 2 2 1
combined immunodeficiency due to ZAP70 deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
EXT2 5 / 11 11p11.2 deletion syndrome, Exostoses, exostoses, multiple, type 2, Potocki-shaffer syndrome and 1 more
ALX4 4 / 11 11p11.2 deletion syndrome, Frontonasal dysplasia with alopecia and genital anomaly, Parietal foramina, Potocki-shaffer syndrome
MSX2 3 / 11 craniosynostosis 2, Parietal foramina, Posterior cortical atrophy
PHF21A 3 / 11 11p11.2 deletion syndrome, Intellectual developmental disorder behavioral dysmorphic, Potocki-shaffer syndrome
ZAP70 2 / 11 combined immunodeficiency due to ZAP70 deficiency, Posterior cortical atrophy
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 ⇵
Defective EXT2 causes exostoses 2
EXT2, EXT1
 Reactome 2 / 14 39.9× 1.11e-3 1.46e-2 ✓ sig.
Defective EXT1 causes exostoses 1, TRPS2 and CHDS
EXT2, EXT1
 Reactome 2 / 14 39.9× 1.11e-3 1.46e-2 ✓ sig.
Tie2 Signaling
PTPN11, ANGPT4
 Reactome 2 / 18 31.0× 1.85e-3 2.15e-2 ✓ sig.
Pink/Parkin Mediated Mitophagy
PRKN, TOMM40
 Reactome 2 / 22 25.4× 2.76e-3 2.90e-2 ✓ sig.
Glycosaminoglycan biosynthesis - heparan sulfate / heparin
EXT2, EXT1
 KEGG 2 / 24 23.3× 3.29e-3 3.29e-2 ✓ sig.
HS-GAG biosynthesis
EXT2, EXT1
 Reactome 2 / 30 18.6× 5.11e-3 4.44e-2 ✓ sig.
Mitophagy - animal
PRKN, ARIH1, TOMM40
 KEGG 3 / 105 8.0× 6.22e-3 5.06e-2
Defective ABCA1 causes Tangier disease
ABCA1
 Reactome 1 / 2 140× 7.15e-3 5.54e-2
SDK interactions
SDK1
 Reactome 1 / 2 140× 7.15e-3 5.54e-2
GLI proteins bind promoters of Hh responsive genes to promote transcription
GLI2
 Reactome 1 / 3 93.1× 1.07e-2 7.16e-2
Catecholamine biosynthesis
DDC
 Reactome 1 / 4 69.8× 1.42e-2 8.45e-2
Serotonin and melatonin biosynthesis
DDC
 Reactome 1 / 5 55.9× 1.78e-2 9.66e-2
MET activates PTPN11
PTPN11
 Reactome 1 / 5 55.9× 1.78e-2 9.66e-2
tRNA modification in the mitochondrion
PUS1
 Reactome 1 / 6 46.6× 2.13e-2 1.07e-1
HDL assembly
ABCA1
 Reactome 1 / 8 34.9× 2.83e-2 1.25e-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 ⇵
fluid transport
EXT2, EXT1
 GO:0042044 2 / 3 290× 1.55e-5 7.38e-4 ✓ sig.
outflow tract septum morphogenesis
ZFPM2, MSX2, SEMA3C
 GO:0003148 3 / 28 46.6× 3.57e-5 1.40e-3 ✓ sig.
embryonic forelimb morphogenesis
ALX4, LNPK, MSX2
 GO:0035115 3 / 33 39.5× 5.90e-5 2.03e-3 ✓ sig.
endochondral bone morphogenesis
EXT2, EXT1
 GO:0060350 2 / 6 145× 7.71e-5 2.50e-3 ✓ sig.
polysaccharide biosynthetic process
EXT2, EXT1
 GO:0000271 2 / 7 124× 1.08e-4 3.20e-3 ✓ sig.
vasodilation
EXT2, EXT1, PTPN11
 GO:0042311 3 / 50 26.1× 2.06e-4 5.16e-3 ✓ sig.
endochondral bone growth
EXT1, MSX2
 GO:0003416 2 / 10 86.9× 2.30e-4 5.57e-3 ✓ sig.
heparin proteoglycan biosynthetic process
EXT2, EXT1
 GO:0030210 2 / 11 79.0× 2.81e-4 6.41e-3 ✓ sig.
embryonic digit morphogenesis
ALX4, LNPK, MSX2
 GO:0042733 3 / 57 22.9× 3.05e-4 6.79e-3 ✓ sig.
multicellular organismal-level water homeostasis
EXT2, EXT1
 GO:0050891 2 / 12 72.4× 3.36e-4 7.26e-3 ✓ sig.
heart development
GLI2, PTPN11, ZFPM2, MAP2K5, SEMA3C
 GO:0007507 5 / 273 8.0× 3.92e-4 8.09e-3 ✓ sig.
outflow tract morphogenesis
ZFPM2, MSX2, SEMA3C
 GO:0003151 3 / 63 20.7× 4.09e-4 8.35e-3 ✓ sig.
osteoblast development
GLI2, MSX2
 GO:0002076 2 / 16 54.3× 6.08e-4 1.10e-2 ✓ sig.
mitochondrial fission
MFF, PRKN
 GO:0000266 2 / 16 54.3× 6.08e-4 1.10e-2 ✓ sig.
sulfation
EXT2, EXT1
 GO:0051923 2 / 16 54.3× 6.08e-4 1.10e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
11p11.2 deletion syndrome Potocki-shaffer syndrome 0.750 3 1.64e-12 2.04e-11 ✓ sig.
exostoses, multiple, type 2 Seizures, scoliosis, and macrocephaly/microcephaly syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Frontonasal dysplasia with alopecia and genital anomaly Parietal foramina 0.333 1 1.30e-4 3.90e-4 ✓ sig.
craniosynostosis 2 Parietal foramina 0.333 1 1.30e-4 3.90e-4 ✓ sig.
11p11.2 deletion syndrome Frontonasal dysplasia with alopecia and genital anomaly 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Potocki-shaffer syndrome Seizures, scoliosis, and macrocephaly/microcephaly syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Intellectual developmental disorder behavioral dysmorphic Potocki-shaffer syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Frontonasal dysplasia with alopecia and genital anomaly Potocki-shaffer syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
exostoses, multiple, type 2 Potocki-shaffer syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
11p11.2 deletion syndrome Intellectual developmental disorder behavioral dysmorphic 0.250 1 1.95e-4 5.28e-4 ✓ sig.
11p11.2 deletion syndrome exostoses, multiple, type 2 0.250 1 1.95e-4 5.28e-4 ✓ sig.
11p11.2 deletion syndrome Seizures, scoliosis, and macrocephaly/microcephaly syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
11p11.2 deletion syndrome Parietal foramina 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Parietal foramina Potocki-shaffer syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
craniosynostosis 2 Posterior cortical atrophy 0.071 1 8.44e-4 1.48e-3 ✓ sig.
combined immunodeficiency due to ZAP70 deficiency Posterior cortical atrophy 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Parietal foramina Posterior cortical atrophy 0.067 1 1.69e-3 2.51e-3 ✓ sig.
Exostoses exostoses, multiple, type 2 0.034 1 1.82e-3 2.66e-3 ✓ sig.
Exostoses Seizures, scoliosis, and macrocephaly/microcephaly syndrome 0.034 1 1.82e-3 2.66e-3 ✓ sig.