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 25

20 diseases · 37 shared-gene connections
20 Diseases
43 Unique genes
0.242 Avg. similarity score
Commissural facial cleft Most-connected disease (7 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 ⇵
Commissural facial cleft 7 7 5
Cataract-corneal dystrophy syndrome 6 6 1
Cleft eyelid 6 6 4
Congenital iris coloboma 6 6 5
PAX6-related ocular dysgenesis 6 6 1
Congenital ocular coloboma 5 5 26
Optic nerve disorder 5 5 2
Tessier facial cleft 5 5 2
Duplication of pituitary gland 4 4 1
Gorlin syndrome 4 4 4
Auriculocondylar syndrome 3 3 4
Coloboma 3 3 15
Paranoid schizophrenia 3 3 4
nevoid basal cell carcinoma syndrome 3 3 2
Opitz g/bbb syndrome 2 2 1
Urinary retention 2 2 1
Arthrogryposis with oculomotor limitation and retinal anomalies 1 1 1
Cataract-microcornea-metabolic syndrome 1 1 1
Neurooculocardio-genitourinary syndrome 1 1 1
auriculocondylar syndrome 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PAX6 9 / 20 Cataract-corneal dystrophy syndrome, Cleft eyelid, Coloboma, Commissural facial cleft and 5 more
PTCH2 5 / 20 Commissural facial cleft, Duplication of pituitary gland, Gorlin syndrome, nevoid basal cell carcinoma syndrome and 1 more
SALL2 5 / 20 Cleft eyelid, Coloboma, Commissural facial cleft, Congenital iris coloboma and 1 more
FZD5 4 / 20 Cleft eyelid, Coloboma, Congenital iris coloboma, Congenital ocular coloboma
ABCB6 3 / 20 Cleft eyelid, Coloboma, Congenital iris coloboma
ACTG1 3 / 20 Coloboma, Congenital iris coloboma, Congenital ocular coloboma
EDN1 3 / 20 Auriculocondylar syndrome, Optic nerve disorder, Urinary retention
SPECC1L 3 / 20 Commissural facial cleft, Opitz g/bbb syndrome, Tessier facial cleft
ACTB 2 / 20 Coloboma, Congenital ocular coloboma
ALDH7A1 2 / 20 Coloboma, Congenital ocular coloboma
ELP4 2 / 20 Coloboma, Congenital ocular coloboma
LAMB1 2 / 20 Coloboma, Congenital ocular coloboma
MYH10 2 / 20 Coloboma, Congenital ocular coloboma
PIEZO2 2 / 20 Arthrogryposis with oculomotor limitation and retinal anomalies, Gorlin syndrome
PLCB4 2 / 20 Auriculocondylar syndrome, auriculocondylar syndrome 2
PTCH1 2 / 20 Gorlin syndrome, nevoid basal cell carcinoma syndrome
RAX 2 / 20 Coloboma, Congenital ocular coloboma
SLBP 2 / 20 Coloboma, Congenital ocular coloboma
SLC16A12 2 / 20 Cataract-microcornea-metabolic syndrome, Congenital ocular coloboma
WDR37 2 / 20 Congenital ocular coloboma, Neurooculocardio-genitourinary syndrome
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 ⇵
Hedgehog signaling pathway
GLI2, PTCH2, CDON, PTCH1, SUFU
 KEGG 5 / 56 24.9× 1.54e-6 7.08e-5 ✓ sig.
Pathways in cancer
EDN1, GNAI3, PLCB4, FZD5, LAMB1, GLI2, MITF, PTCH2, RARB, PTCH1, SUFU
 KEGG 11 / 533 5.8× 1.87e-6 8.32e-5 ✓ sig.
Basal cell carcinoma
FZD5, GLI2, PTCH2, PTCH1, SUFU
 KEGG 5 / 63 22.2× 2.79e-6 1.17e-4 ✓ sig.
Melanogenesis
EDN1, GNAI3, PLCB4, FZD5, MITF
 KEGG 5 / 101 13.8× 2.84e-5 7.97e-4 ✓ sig.
Gastric acid secretion
GNAI3, PLCB4, ACTB, ACTG1
 KEGG 4 / 76 14.7× 1.52e-4 3.14e-3 ✓ sig.
Hippo signaling pathway
FZD5, ACTB, ACTG1, GLI2, YAP1
 KEGG 5 / 157 8.9× 2.31e-4 4.38e-3 ✓ sig.
Ligand-receptor interactions
CDON, PTCH1
 Reactome 2 / 7 79.8× 2.60e-4 4.79e-3 ✓ sig.
Recycling pathway of L1
DPYSL2, ACTB, ACTG1
 Reactome 3 / 40 20.9× 3.85e-4 6.52e-3 ✓ sig.
Formation of annular gap junctions
ACTB, ACTG1
 Reactome 2 / 11 50.8× 6.75e-4 1.01e-2 ✓ sig.
Cell-extracellular matrix interactions
ACTB, ACTG1
 Reactome 2 / 12 46.6× 8.08e-4 1.16e-2 ✓ sig.
Gap junction degradation
ACTB, ACTG1
 Reactome 2 / 12 46.6× 8.08e-4 1.16e-2 ✓ sig.
PLC beta mediated events
GNAI3, PLCB4
 Reactome 2 / 12 46.6× 8.08e-4 1.16e-2 ✓ sig.
Interaction between L1 and Ankyrins
ACTB, ACTG1
 Reactome 2 / 13 43.0× 9.53e-4 1.31e-2 ✓ sig.
Hedgehog 'off' state
GLI2, PTCH1, SUFU
 Reactome 3 / 56 15.0× 1.04e-3 1.40e-2 ✓ sig.
Platelet activation
GNAI3, PLCB4, ACTB, ACTG1
 KEGG 4 / 126 8.9× 1.04e-3 1.40e-2 ✓ 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 ⇵
camera-type eye development
PAX6, RAX, CHD7, MITF, MAB21L2, PAX2
 GO:0043010 6 / 74 35.2× 1.70e-8 2.72e-6 ✓ sig.
cell fate determination
PAX6, PTCH2, PAX2, PTCH1
 GO:0001709 4 / 18 96.6× 7.26e-8 9.21e-6 ✓ sig.
eye development
PAX6, FZD5, SALL2, MAB21L2, RBP4
 GO:0001654 5 / 49 44.3× 8.98e-8 1.10e-5 ✓ sig.
brain development
PAX6, ABCB6, MYH10, RAX, DHX37, CDK5RAP2, PTCH1
 GO:0007420 7 / 244 12.5× 1.28e-6 1.01e-4 ✓ sig.
axonogenesis
PAX6, ACTB, ACTG1, MYH10, PAX2
 GO:0007409 5 / 125 17.4× 9.70e-6 5.10e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
EDN1, PAX6, FZD5, SALL2, RAX, GLI2, CHD7, MITF, CDON, PAX2, RARB, YAP1
 GO:0045944 12 / 1,208 4.3× 1.19e-5 5.95e-4 ✓ sig.
postsynaptic actin cytoskeleton organization
ACTB, ACTG1, MYH10
 GO:0098974 3 / 20 65.2× 1.26e-5 6.25e-4 ✓ sig.
smoothened signaling pathway involved in ventral spinal cord interneuron specification
GLI2, SUFU
 GO:0021775 2 / 3 290× 1.55e-5 7.38e-4 ✓ sig.
regulation of transepithelial transport
ACTB, ACTG1
 GO:0150111 2 / 4 217× 3.09e-5 1.25e-3 ✓ sig.
retina development in camera-type eye
PAX6, MYH10, CHD7, RBP4
 GO:0060041 4 / 85 20.5× 4.30e-5 1.61e-3 ✓ sig.
epidermal cell fate specification
PTCH2, PTCH1
 GO:0009957 2 / 5 174× 5.15e-5 1.84e-3 ✓ sig.
regulation of metanephric nephron tubule epithelial cell differentiation
PAX2, YAP1
 GO:0072307 2 / 5 174× 5.15e-5 1.84e-3 ✓ sig.
regulation of neuron differentiation
PAX6, CDK5RAP2, CDON
 GO:0045664 3 / 32 40.7× 5.37e-5 1.90e-3 ✓ sig.
aorta development
MYH10, CHD7, SUFU
 GO:0035904 3 / 33 39.5× 5.90e-5 2.03e-3 ✓ sig.
neural precursor cell proliferation
PAX6, CDON, RARB
 GO:0061351 3 / 33 39.5× 5.90e-5 2.03e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Coloboma Congenital ocular coloboma 0.355 11 3.65e-29 1.14e-27 ✓ sig.
Coloboma Congenital iris coloboma 0.313 5 4.17e-16 6.78e-15 ✓ sig.
Cleft eyelid Congenital iris coloboma 0.667 4 2.14e-15 3.30e-14 ✓ sig.
Cleft eyelid Coloboma 0.250 4 5.83e-13 7.60e-12 ✓ sig.
Congenital iris coloboma Congenital ocular coloboma 0.143 4 3.19e-11 3.53e-10 ✓ sig.
Cleft eyelid Congenital ocular coloboma 0.107 3 1.71e-8 1.42e-7 ✓ sig.
Gorlin syndrome nevoid basal cell carcinoma syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Commissural facial cleft Tessier facial cleft 0.333 2 8.44e-8 6.27e-7 ✓ sig.
Cleft eyelid Commissural facial cleft 0.250 2 5.06e-7 3.32e-6 ✓ sig.
Commissural facial cleft Congenital iris coloboma 0.222 2 8.43e-7 5.28e-6 ✓ sig.
Cataract-corneal dystrophy syndrome PAX6-related ocular dysgenesis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Duplication of pituitary gland Tessier facial cleft 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Optic nerve disorder 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Duplication of pituitary gland nevoid basal cell carcinoma syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Opitz g/bbb syndrome Tessier facial cleft 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Optic nerve disorder Urinary retention 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Optic nerve disorder PAX6-related ocular dysgenesis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
nevoid basal cell carcinoma syndrome Tessier facial cleft 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Arthrogryposis with oculomotor limitation and retinal anomalies Gorlin syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cleft eyelid PAX6-related ocular dysgenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Cleft eyelid 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Paranoid schizophrenia 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Paranoid schizophrenia PAX6-related ocular dysgenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Duplication of pituitary gland Gorlin syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Auriculocondylar syndrome auriculocondylar syndrome 2 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Auriculocondylar syndrome Urinary retention 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Commissural facial cleft Opitz g/bbb syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Congenital iris coloboma 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Commissural facial cleft Duplication of pituitary gland 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital iris coloboma PAX6-related ocular dysgenesis 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Commissural facial cleft PAX6-related ocular dysgenesis 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cataract-corneal dystrophy syndrome Commissural facial cleft 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Gorlin syndrome Tessier facial cleft 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Auriculocondylar syndrome Optic nerve disorder 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Optic nerve disorder Paranoid schizophrenia 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Congenital ocular coloboma Neurooculocardio-genitourinary syndrome 0.037 1 1.69e-3 2.51e-3 ✓ sig.
Cataract-microcornea-metabolic syndrome Congenital ocular coloboma 0.037 1 1.69e-3 2.51e-3 ✓ sig.