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 52

16 diseases · 39 shared-gene connections
16 Diseases
76 Unique genes
0.140 Avg. similarity score
Microphthalmia Most-connected disease (12 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 ⇵
Microphthalmia 12 12 38
Colobomatous microphthalmia 10 10 15
Microphthalmos 9 9 36
Nanophthalmos 8 8 12
Anophthalmia/microphthalmia-esophageal atresia syndrome 6 6 25
Congenital cystic eyeball 6 6 6
Anophthalmia 4 4 14
Colobomatous optic disc macular atrophy chorioretinopathy syndrome 4 4 2
Focal dermal hypoplasia 4 4 1
isolated microphthalmia 6 4 4 1
Klippel-feil syndrome 3 3 7
Microphthalmia with retinitis pigmentosa and ocular anomalies 3 3 2
colobomatous microphthalmia-rhizomelic dysplasia syndrome 2 2 1
Klippel-Feil anomaly-myopathy-facial dysmorphism syndrome 1 1 1
X-linked colobomatous microphthalmia, microcephaly, intellectual disability, short stature syndrome 1 1 1
nanophthalmos 4 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RAX 7 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Congenital cystic eyeball and 3 more
OTX2 6 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Microphthalmia and 2 more
SOX2 6 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Microphthalmia and 2 more
VSX2 6 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Congenital cystic eyeball and 2 more
ALDH1A3 5 / 16 Colobomatous microphthalmia, Congenital cystic eyeball, Microphthalmia, Microphthalmos and 1 more
GDF3 5 / 16 Colobomatous microphthalmia, Congenital cystic eyeball, Klippel-feil syndrome, Microphthalmia and 1 more
GDF6 5 / 16 Colobomatous microphthalmia, Congenital cystic eyeball, Klippel-feil syndrome, Microphthalmia and 1 more
PORCN 5 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Focal dermal hypoplasia, Microphthalmia and 1 more
PRSS56 5 / 16 Congenital cystic eyeball, isolated microphthalmia 6, Microphthalmia, Microphthalmos and 1 more
SIX6 5 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Colobomatous optic disc macular atrophy chorioretinopathy syndrome, Microphthalmia and 1 more
STRA6 5 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous microphthalmia, Microphthalmia and 1 more
MFRP 4 / 16 Microphthalmia, Microphthalmia with retinitis pigmentosa and ocular anomalies, Microphthalmos, Nanophthalmos
PAX6 4 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome, Microphthalmia, Microphthalmos
RBP4 4 / 16 Anophthalmia, Colobomatous microphthalmia, Microphthalmia, Microphthalmos
ABCB6 3 / 16 Colobomatous microphthalmia, Microphthalmia, Microphthalmos
C14ORF39 3 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Colobomatous optic disc macular atrophy chorioretinopathy syndrome, Microphthalmia
C1QTNF5 3 / 16 Microphthalmia, Microphthalmia with retinitis pigmentosa and ocular anomalies, Nanophthalmos
MAB21L2 3 / 16 Colobomatous microphthalmia, colobomatous microphthalmia-rhizomelic dysplasia syndrome, Microphthalmia
RARB 3 / 16 Anophthalmia, Microphthalmia, Microphthalmos
SHH 3 / 16 Colobomatous microphthalmia, Microphthalmia, Microphthalmos
TENM3 3 / 16 Colobomatous microphthalmia, Microphthalmia, Microphthalmos
VAX1 3 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Microphthalmia, Microphthalmos
ARHGAP35 2 / 16 Anophthalmia, Microphthalmos
BMP4 2 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Microphthalmia
ELP4 2 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome
HCCS 2 / 16 Microphthalmia, Microphthalmos
HMGB3 2 / 16 Microphthalmia, X-linked colobomatous microphthalmia, microcephaly, intellectual disability, short stature syndrome
HMX1 2 / 16 Microphthalmia, Microphthalmos
MYO18B 2 / 16 Klippel-Feil anomaly-myopathy-facial dysmorphism syndrome, Klippel-feil syndrome
PITX3 2 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Microphthalmos
SMOC1 2 / 16 Anophthalmia, Microphthalmia
TFAP2A 2 / 16 Anophthalmia/microphthalmia-esophageal atresia syndrome, Microphthalmos
TMEM98 2 / 16 Nanophthalmos, nanophthalmos 4
WNT7B 2 / 16 Anophthalmia, Anophthalmia/microphthalmia-esophageal atresia syndrome
ZNF219 2 / 16 Microphthalmia, Microphthalmos
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 ⇵
Basal cell carcinoma
WNT7B, BMP4, PTCH1, SHH, FZD5
 KEGG 5 / 63 12.5× 4.69e-5 1.21e-3 ✓ sig.
TFAP2 (AP-2) family regulates transcription of other transcription factors
PITX2, TFAP2A
 Reactome 2 / 4 79.0× 2.35e-4 4.44e-3 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
WNT7B, SOX2, BMP4, HESX1, PAX6, FZD5
 KEGG 6 / 144 6.6× 2.94e-4 5.27e-3 ✓ sig.
Gastric cancer
RARB, WNT7B, SHH, FZD5, FGF8, LRP5
 KEGG 6 / 150 6.3× 3.66e-4 6.26e-3 ✓ sig.
Hippo signaling pathway
WNT7B, SOX2, BMP4, GDF6, FZD5, CRB1
 KEGG 6 / 157 6.0× 4.66e-4 7.55e-3 ✓ sig.
Ligand-receptor interactions
PTCH1, SHH
 Reactome 2 / 7 45.2× 8.13e-4 1.16e-2 ✓ sig.
RNF mutants show enhanced WNT signaling and proliferation
FZD5, LRP5
 Reactome 2 / 8 39.5× 1.08e-3 1.44e-2 ✓ sig.
Retinoid cycle disease events
STRA6, RBP4
 Reactome 2 / 13 24.3× 2.95e-3 3.04e-2 ✓ sig.
Activation of SMO
PTCH1, SHH
 Reactome 2 / 18 17.6× 5.66e-3 4.75e-2 ✓ sig.
Pathways in cancer
RARB, WNT7B, BMP4, IKBKG, PTCH1, SHH, FZD5, FGF8, LRP5
 KEGG 9 / 533 2.7× 6.30e-3 5.10e-2
Defective ABCB6 causes isolated colobomatous microphthalmia 7 (MCOPCB7)
ABCB6
 Reactome 1 / 1 158× 6.33e-3 5.11e-2
Retinoid metabolism disease events
RBP4
 Reactome 1 / 1 158× 6.33e-3 5.11e-2
WNT ligand secretion is abrogated by the PORCN inhibitor LGK974
PORCN
 Reactome 1 / 1 158× 6.33e-3 5.11e-2
The canonical retinoid cycle in rods (twilight vision)
STRA6, RBP4
 Reactome 2 / 20 15.8× 6.97e-3 5.45e-2
Regulation of FZD by ubiquitination
FZD5, LRP5
 Reactome 2 / 21 15.1× 7.68e-3 5.81e-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
STRA6, BMP4, CRYBA4, HESX1, PAX2, PAX6, PITX2, RAX, SIX3, VAX1, VSX2, ARHGAP35
 GO:0043010 16 / 74 53.2× 5.82e-24 1.63e-20 ✓ sig.
eye development
SIX6, SOX2, PAX6, SIX3, RBP4, SMOC1, GDF3, MAB21L2, FZD5
 GO:0001654 9 / 49 45.2× 3.36e-13 1.69e-10 ✓ sig.
visual perception
SIX6, CRYBA4, PAX2, PAX6, RAX, SIX3, VSX2, RBP4, MFRP, CRYBB3, MIP, BEST1
 GO:0007601 13 / 215 14.9× 3.47e-12 1.41e-9 ✓ sig.
lens development in camera-type eye
CRYBA4, NHS, PAX6, PITX3, SIX3, CRYBB3, GJA8, MIP
 GO:0002088 8 / 48 41.0× 1.70e-11 5.91e-9 ✓ sig.
pituitary gland development
SOX2, BMP4, HESX1, PAX6, PITX2, SIX3
 GO:0021983 6 / 30 49.2× 2.03e-9 4.19e-7 ✓ sig.
telencephalon regionalization
BMP4, PAX6, SIX3, SHH
 GO:0021978 4 / 7 141× 8.76e-9 1.53e-6 ✓ sig.
forebrain development
SOX2, BMP4, HESX1, OTX2, PAX6, ARHGAP35, SHH
 GO:0030900 7 / 76 22.6× 2.42e-8 3.68e-6 ✓ sig.
metanephric collecting duct development
WNT7B, PAX2, PTCH1, SHH
 GO:0072205 4 / 9 109× 3.13e-8 4.55e-6 ✓ sig.
negative regulation of transcription by RNA polymerase II
RARB, SOX2, BMP4, DACH1, HESX1, PAX6, PITX2, PTCH1, TFAP2A, VAX1, VSX2, TBX18
 GO:0000122 18 / 1,002 4.4× 7.53e-8 9.49e-6 ✓ sig.
embryonic hindlimb morphogenesis
RARB, BMP4, PITX2, SHH, FGF8
 GO:0035116 5 / 29 42.4× 1.07e-7 1.28e-5 ✓ sig.
positive regulation of transcription by RNA polymerase II
RARB, SOX2, BMP4, IKBKG, OTX2, PAX2, PAX6, PITX2, PITX3, RAX, SIX3, TFAP2A
 GO:0045944 19 / 1,208 3.9× 2.43e-7 2.55e-5 ✓ sig.
lung development
STRA6, WNT7B, BMP4, PITX2, RBP4, SHH, FGF8
 GO:0030324 7 / 108 15.9× 2.79e-7 2.87e-5 ✓ sig.
odontogenesis
BMP4, PITX2, SHH, BCOR, FGF8
 GO:0042476 5 / 36 34.2× 3.33e-7 3.32e-5 ✓ sig.
smooth muscle tissue development
STRA6, BMP4, PTCH1, SHH
 GO:0048745 4 / 16 61.5× 4.43e-7 4.22e-5 ✓ sig.
positive regulation of DNA-templated transcription
SOX2, BMP4, OTX2, PAX2, PAX6, PITX2, PITX3, PTCH1, TFAP2A, TBX18, GDF6, SHH
 GO:0045893 15 / 778 4.7× 4.54e-7 4.31e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Microphthalmia Microphthalmos 0.389 21 9.45e-49 5.08e-47 ✓ sig.
Colobomatous microphthalmia Microphthalmia 0.385 15 3.14e-41 1.43e-39 ✓ sig.
Colobomatous microphthalmia Microphthalmos 0.333 13 5.54e-34 2.05e-32 ✓ sig.
Anophthalmia/microphthalmia-esophageal atresia syndrome Microphthalmia 0.208 11 1.82e-23 4.33e-22 ✓ sig.
Anophthalmia Microphthalmos 0.214 9 1.40e-21 3.02e-20 ✓ sig.
Anophthalmia Microphthalmia 0.205 9 2.42e-21 5.16e-20 ✓ sig.
Anophthalmia/microphthalmia-esophageal atresia syndrome Microphthalmos 0.192 10 3.94e-21 8.36e-20 ✓ sig.
Anophthalmia Anophthalmia/microphthalmia-esophageal atresia syndrome 0.250 8 4.13e-20 8.38e-19 ✓ sig.
Microphthalmia Nanophthalmos 0.186 8 3.07e-19 5.91e-18 ✓ sig.
Anophthalmia/microphthalmia-esophageal atresia syndrome Colobomatous microphthalmia 0.206 7 7.54e-17 1.29e-15 ✓ sig.
Congenital cystic eyeball Microphthalmos 0.162 6 1.05e-16 1.79e-15 ✓ sig.
Congenital cystic eyeball Microphthalmia 0.154 6 1.49e-16 2.51e-15 ✓ sig.
Anophthalmia Colobomatous microphthalmia 0.250 6 8.09e-16 1.29e-14 ✓ sig.
Colobomatous microphthalmia Congenital cystic eyeball 0.294 5 2.50e-15 3.84e-14 ✓ sig.
Microphthalmos Nanophthalmos 0.140 6 9.63e-14 1.32e-12 ✓ sig.
Colobomatous microphthalmia Nanophthalmos 0.217 5 3.29e-13 4.39e-12 ✓ sig.
Congenital cystic eyeball Nanophthalmos 0.188 3 7.22e-9 6.36e-8 ✓ sig.
Microphthalmia with retinitis pigmentosa and ocular anomalies Nanophthalmos 0.154 2 5.57e-7 3.60e-6 ✓ sig.
Anophthalmia/microphthalmia-esophageal atresia syndrome Colobomatous optic disc macular atrophy chorioretinopathy syndrome 0.077 2 2.53e-6 1.46e-5 ✓ sig.
Congenital cystic eyeball Klippel-feil syndrome 0.167 2 2.65e-6 1.53e-5 ✓ sig.
Colobomatous optic disc macular atrophy chorioretinopathy syndrome Microphthalmia 0.051 2 5.93e-6 3.21e-5 ✓ sig.
Microphthalmia Microphthalmia with retinitis pigmentosa and ocular anomalies 0.051 2 5.93e-6 3.21e-5 ✓ sig.
Colobomatous microphthalmia Klippel-feil syndrome 0.095 2 1.85e-5 9.34e-5 ✓ sig.
Congenital cystic eyeball isolated microphthalmia 6 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Klippel-Feil anomaly-myopathy-facial dysmorphism syndrome Klippel-feil syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
isolated microphthalmia 6 Nanophthalmos 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Nanophthalmos nanophthalmos 4 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Colobomatous microphthalmia Focal dermal hypoplasia 0.063 1 9.74e-4 1.64e-3 ✓ sig.
Colobomatous microphthalmia colobomatous microphthalmia-rhizomelic dysplasia syndrome 0.063 1 9.74e-4 1.64e-3 ✓ sig.
Colobomatous optic disc macular atrophy chorioretinopathy syndrome Nanophthalmos 0.071 1 1.56e-3 2.36e-3 ✓ sig.
Anophthalmia/microphthalmia-esophageal atresia syndrome Focal dermal hypoplasia 0.038 1 1.62e-3 2.44e-3 ✓ sig.
Colobomatous microphthalmia Colobomatous optic disc macular atrophy chorioretinopathy syndrome 0.059 1 1.95e-3 2.81e-3 ✓ sig.
isolated microphthalmia 6 Microphthalmos 0.027 1 2.34e-3 3.23e-3 ✓ sig.
Focal dermal hypoplasia Microphthalmos 0.027 1 2.34e-3 3.23e-3 ✓ sig.
isolated microphthalmia 6 Microphthalmia 0.026 1 2.47e-3 3.36e-3 ✓ sig.
Focal dermal hypoplasia Microphthalmia 0.026 1 2.47e-3 3.36e-3 ✓ sig.
colobomatous microphthalmia-rhizomelic dysplasia syndrome Microphthalmia 0.026 1 2.47e-3 3.36e-3 ✓ sig.
Microphthalmia X-linked colobomatous microphthalmia, microcephaly, intellectual disability, short stature syndrome 0.026 1 2.47e-3 3.36e-3 ✓ sig.
Microphthalmia with retinitis pigmentosa and ocular anomalies Microphthalmos 0.026 1 4.67e-3 5.78e-3 ✓ sig.