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 48

15 diseases · 38 shared-gene connections
15 Diseases
49 Unique genes
0.302 Avg. similarity score
Apert syndrome Most-connected disease (8 links)
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Disease Searched: Goldenhar syndrome 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 ⇵
Apert syndrome 8 8 5
Congenital malformation syndromes predominantly affecting facial appearance 8 8 4
Cryptophthalmos syndrome 8 8 7
Goldenhar syndrome 8 8 10
Warburg micro syndrome 8 8 4
Cyclocephaly 7 7 7
Cataract-intellectual disability-hypogonadism syndrome 6 6 2
Craniofacial microsomia 5 5 15
Mobius syndrome 5 5 15
Martsolf syndrome 4 4 10
Hemifacial microsomia 3 3 4
T-cell immunodeficiency 3 3 1
Corpus callosum agenesis with facial anomalies and cerebellar ataxia 1 1 1
Intestinal dysmotility syndrome 1 1 1
fraser syndrome 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RAB3GAP1 9 / 15 Apert syndrome, Cataract-intellectual disability-hypogonadism syndrome, Congenital malformation syndromes predominantly affecting facial appearance, Cryptophthalmos syndrome and 5 more
RAB3GAP2 9 / 15 Apert syndrome, Cataract-intellectual disability-hypogonadism syndrome, Congenital malformation syndromes predominantly affecting facial appearance, Cryptophthalmos syndrome and 5 more
RAB18 7 / 15 Apert syndrome, Congenital malformation syndromes predominantly affecting facial appearance, Cryptophthalmos syndrome, Cyclocephaly and 3 more
TBC1D20 7 / 15 Apert syndrome, Congenital malformation syndromes predominantly affecting facial appearance, Cryptophthalmos syndrome, Cyclocephaly and 3 more
FOXI3 4 / 15 Craniofacial microsomia, Goldenhar syndrome, Hemifacial microsomia, T-cell immunodeficiency
SF3B2 3 / 15 Craniofacial microsomia, Goldenhar syndrome, Hemifacial microsomia
AMIGO2 2 / 15 Craniofacial microsomia, Goldenhar syndrome
ANO1 2 / 15 Craniofacial microsomia, Intestinal dysmotility syndrome
FRMD4A 2 / 15 Corpus callosum agenesis with facial anomalies and cerebellar ataxia, Craniofacial microsomia
GRIP1 2 / 15 Cryptophthalmos syndrome, fraser syndrome 3
MYT1 2 / 15 Craniofacial microsomia, Goldenhar 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 ⇵
PI3K Cascade
FGFR2, FGF3, FGF8, FGFR1, KLB
 Reactome 5 / 39 31.4× 4.76e-7 2.74e-5 ✓ sig.
Negative regulation of FGFR1 signaling
FGF3, FGF8, ANOS1, FGFR1
 Reactome 4 / 26 37.7× 3.42e-6 1.49e-4 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
FGFR2, FGF3, FGF8, FGFR1, KLB
 Reactome 5 / 75 16.3× 1.28e-5 4.35e-4 ✓ sig.
FGFR1c ligand binding and activation
FGF8, ANOS1, FGFR1
 Reactome 3 / 12 61.3× 1.37e-5 4.60e-4 ✓ sig.
Phospholipase C-mediated cascade: FGFR1
FGF3, FGF8, FGFR1
 Reactome 3 / 16 46.0× 3.44e-5 9.84e-4 ✓ sig.
PIP3 activates AKT signaling
FGFR2, FGF3, FGF8, FGFR1, KLB
 Reactome 5 / 93 13.2× 3.64e-5 1.03e-3 ✓ sig.
Activated point mutants of FGFR2
FGFR2, FGF3, FGF8
 Reactome 3 / 17 43.3× 4.17e-5 1.15e-3 ✓ sig.
Phospholipase C-mediated cascade; FGFR2
FGFR2, FGF3, FGF8
 Reactome 3 / 18 40.9× 4.99e-5 1.34e-3 ✓ sig.
Downstream signaling of activated FGFR1
FGF3, FGF8, FGFR1
 Reactome 3 / 18 40.9× 4.99e-5 1.34e-3 ✓ sig.
COPI-independent Golgi-to-ER retrograde traffic
RAB18, RAB3GAP1, RAB3GAP2, TUBB3
 Reactome 4 / 51 19.2× 5.31e-5 1.40e-3 ✓ sig.
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
FGFR2, FGF3, FGF8, FGFR1, KLB
 Reactome 5 / 103 11.9× 5.95e-5 1.53e-3 ✓ sig.
PI-3K cascade:FGFR1
FGF3, FGF8, FGFR1
 Reactome 3 / 21 35.0× 8.06e-5 1.96e-3 ✓ sig.
SHC-mediated cascade:FGFR1
FGF3, FGF8, FGFR1
 Reactome 3 / 21 35.0× 8.06e-5 1.96e-3 ✓ sig.
FRS-mediated FGFR1 signaling
FGF3, FGF8, FGFR1
 Reactome 3 / 23 32.0× 1.07e-4 2.45e-3 ✓ sig.
PI-3K cascade:FGFR2
FGFR2, FGF3, FGF8
 Reactome 3 / 23 32.0× 1.07e-4 2.45e-3 ✓ 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 ⇵
fibroblast growth factor receptor signaling pathway
FGFR2, FGF3, FGF8, FGFR1, KLB
 GO:0008543 5 / 60 31.8× 4.93e-7 4.73e-5 ✓ sig.
branching involved in salivary gland morphogenesis
FGFR2, FGF8, FGFR1
 GO:0060445 3 / 12 95.3× 3.67e-6 2.42e-4 ✓ sig.
negative regulation of cardiac muscle tissue development
FGF3, FGF8
 GO:0055026 2 / 2 381× 6.74e-6 3.94e-4 ✓ sig.
fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development
FGFR2, FGFR1
 GO:0035607 2 / 2 381× 6.74e-6 3.94e-4 ✓ sig.
lipid droplet organization
RAB18, RAB3GAP1, TBC1D20
 GO:0034389 3 / 18 63.6× 1.34e-5 6.82e-4 ✓ sig.
orbitofrontal cortex development
FGFR2, FGFR1
 GO:0021769 2 / 3 254× 2.02e-5 9.34e-4 ✓ sig.
ventricular zone neuroblast division
FGFR2, FGFR1
 GO:0021847 2 / 3 254× 2.02e-5 9.34e-4 ✓ sig.
establishment of protein localization to endoplasmic reticulum membrane
RAB3GAP1, RAB3GAP2
 GO:0097051 2 / 3 254× 2.02e-5 9.34e-4 ✓ sig.
positive regulation of endoplasmic reticulum tubular network organization
RAB3GAP1, RAB3GAP2
 GO:1903373 2 / 3 254× 2.02e-5 9.34e-4 ✓ sig.
motor neuron axon guidance
FGF8, SEMA3A, CHN1
 GO:0008045 3 / 24 47.7× 3.30e-5 1.36e-3 ✓ sig.
positive regulation of phospholipase activity
FGFR2, FGFR1
 GO:0010518 2 / 4 191× 4.03e-5 1.58e-3 ✓ sig.
positive regulation of protein lipidation
RAB3GAP1, RAB3GAP2
 GO:1903061 2 / 4 191× 4.03e-5 1.58e-3 ✓ sig.
positive regulation of mesenchymal cell proliferation
FGFR2, ARHGAP5, FGFR1
 GO:0002053 3 / 26 44.0× 4.22e-5 1.64e-3 ✓ sig.
cell fate commitment
FGFR2, FGF8, GAS1, KDM6B
 GO:0045165 4 / 75 20.3× 4.42e-5 1.70e-3 ✓ sig.
anatomical structure morphogenesis
FGF3, FOXI3, FREM2, FRAS1, FGF8
 GO:0009653 5 / 160 11.9× 6.08e-5 2.15e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital malformation syndromes predominantly affecting facial appearance Warburg micro syndrome 0.800 4 4.27e-16 6.52e-15 ✓ sig.
Apert syndrome Warburg micro syndrome 0.667 4 2.14e-15 3.12e-14 ✓ sig.
Apert syndrome Congenital malformation syndromes predominantly affecting facial appearance 0.667 4 2.14e-15 3.12e-14 ✓ sig.
Cryptophthalmos syndrome Warburg micro syndrome 0.500 4 1.49e-14 2.06e-13 ✓ sig.
Cyclocephaly Warburg micro syndrome 0.500 4 1.49e-14 2.06e-13 ✓ sig.
Congenital malformation syndromes predominantly affecting facial appearance Cyclocephaly 0.500 4 1.49e-14 2.06e-13 ✓ sig.
Congenital malformation syndromes predominantly affecting facial appearance Cryptophthalmos syndrome 0.500 4 1.49e-14 2.06e-13 ✓ sig.
Apert syndrome Cyclocephaly 0.444 4 7.47e-14 9.76e-13 ✓ sig.
Apert syndrome Cryptophthalmos syndrome 0.444 4 7.47e-14 9.76e-13 ✓ sig.
Goldenhar syndrome Warburg micro syndrome 0.364 4 8.97e-14 1.16e-12 ✓ sig.
Congenital malformation syndromes predominantly affecting facial appearance Goldenhar syndrome 0.364 4 8.97e-14 1.16e-12 ✓ sig.
Apert syndrome Goldenhar syndrome 0.333 4 4.48e-13 5.60e-12 ✓ sig.
Cryptophthalmos syndrome Cyclocephaly 0.364 4 5.23e-13 6.47e-12 ✓ sig.
Congenital malformation syndromes predominantly affecting facial appearance Mobius syndrome 0.250 4 5.83e-13 7.18e-12 ✓ sig.
Mobius syndrome Warburg micro syndrome 0.250 4 5.83e-13 7.18e-12 ✓ sig.
Apert syndrome Mobius syndrome 0.235 4 2.91e-12 3.34e-11 ✓ sig.
Cyclocephaly Goldenhar syndrome 0.286 4 3.14e-12 3.58e-11 ✓ sig.
Cryptophthalmos syndrome Goldenhar syndrome 0.286 4 3.14e-12 3.58e-11 ✓ sig.
Cyclocephaly Mobius syndrome 0.211 4 2.04e-11 2.17e-10 ✓ sig.
Cryptophthalmos syndrome Mobius syndrome 0.211 4 2.04e-11 2.17e-10 ✓ sig.
Craniofacial microsomia Goldenhar syndrome 0.182 4 1.22e-10 1.21e-9 ✓ sig.
Cataract-intellectual disability-hypogonadism syndrome Congenital malformation syndromes predominantly affecting facial appearance 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Cataract-intellectual disability-hypogonadism syndrome Warburg micro syndrome 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Apert syndrome Cataract-intellectual disability-hypogonadism syndrome 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Cataract-intellectual disability-hypogonadism syndrome Cyclocephaly 0.250 2 1.77e-7 1.18e-6 ✓ sig.
Cataract-intellectual disability-hypogonadism syndrome Cryptophthalmos syndrome 0.250 2 1.77e-7 1.18e-6 ✓ sig.
Cataract-intellectual disability-hypogonadism syndrome Martsolf syndrome 0.182 2 3.80e-7 2.39e-6 ✓ sig.
Goldenhar syndrome Hemifacial microsomia 0.154 2 2.28e-6 1.26e-5 ✓ sig.
Congenital malformation syndromes predominantly affecting facial appearance Martsolf syndrome 0.154 2 2.28e-6 1.26e-5 ✓ sig.
Martsolf syndrome Warburg micro syndrome 0.154 2 2.28e-6 1.26e-5 ✓ sig.
Apert syndrome Martsolf syndrome 0.143 2 3.79e-6 2.01e-5 ✓ sig.
Craniofacial microsomia Hemifacial microsomia 0.111 2 5.31e-6 2.74e-5 ✓ sig.
Hemifacial microsomia T-cell immunodeficiency 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cryptophthalmos syndrome fraser syndrome 3 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Goldenhar syndrome T-cell immunodeficiency 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Corpus callosum agenesis with facial anomalies and cerebellar ataxia Craniofacial microsomia 0.063 1 9.74e-4 1.67e-3 ✓ sig.
Craniofacial microsomia Intestinal dysmotility syndrome 0.063 1 9.74e-4 1.67e-3 ✓ sig.
Craniofacial microsomia T-cell immunodeficiency 0.063 1 9.74e-4 1.67e-3 ✓ sig.