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 262

7 diseases · 7 shared-gene connections
7 Diseases
284 Unique genes
0.026 Avg. similarity score
Myopia Most-connected disease (5 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 ⇵
Myopia 5 5 133
Hyperopia 3 3 79
Eye disease 2 2 94
Bone marrow failure and diabetes mellitus syndrome 1 1 1
Trichotillomania 1 1 2
cardiomyopathy, dilated, 2j 1 1 1
neurodevelopmental disorder with or without seizures and gait abnormalities 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GJD2 3 / 7 Eye disease, Hyperopia, Myopia
KCNQ5 3 / 7 Eye disease, Hyperopia, Myopia
LAMA2 3 / 7 Eye disease, Hyperopia, Myopia
PRSS56 3 / 7 Eye disease, Hyperopia, Myopia
RDH5 3 / 7 Eye disease, Hyperopia, Myopia
ABCA1 2 / 7 Eye disease, Myopia
C14ORF39 2 / 7 Eye disease, Hyperopia
CHD7 2 / 7 Hyperopia, Myopia
DUT 2 / 7 Bone marrow failure and diabetes mellitus syndrome, Myopia
EFEMP1 2 / 7 Eye disease, Myopia
FLII 2 / 7 cardiomyopathy, dilated, 2j, Myopia
GRIA4 2 / 7 Myopia, neurodevelopmental disorder with or without seizures and gait abnormalities
HLA-DQB1 2 / 7 Eye disease, Myopia
IRX5 2 / 7 Hyperopia, Myopia
LRP2 2 / 7 Eye disease, Myopia
RASGEF1B 2 / 7 Eye disease, Hyperopia
RASGRF1 2 / 7 Hyperopia, Myopia
RBFOX1 2 / 7 Eye disease, Hyperopia
RGR 2 / 7 Eye disease, Hyperopia
SHISA6 2 / 7 Eye disease, Hyperopia
SLITRK1 2 / 7 Hyperopia, Trichotillomania
TYR 2 / 7 Eye disease, Myopia
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 ⇵
MET activates PTK2 signaling
COL24A1, COL5A1, LAMA2, LAMB1, COL11A1, COL2A1, HGF, LAMA5
 Reactome 8 / 30 11.3× 3.30e-7 1.86e-5 ✓ sig.
Collagen biosynthesis and modifying enzymes
COL24A1, COL5A1, COL11A1, COL2A1, COL4A4, COL9A1, P3H2, P4HA2, COL17A1, COL18A1
 Reactome 10 / 67 6.3× 3.52e-6 1.42e-4 ✓ sig.
Collagen chain trimerization
COL24A1, COL5A1, COL11A1, COL2A1, COL4A4, COL9A1, COL17A1, COL18A1
 Reactome 8 / 44 7.7× 7.50e-6 2.63e-4 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL24A1, COL5A1, COL11A1, COL2A1, COL4A4, COL9A1, COL17A1, COL18A1
 Reactome 8 / 51 6.6× 2.33e-5 6.78e-4 ✓ sig.
Protein digestion and absorption
COL24A1, COL5A1, FXYD2, COL11A1, COL2A1, COL4A4, COL9A1, COL17A1, COL18A1, SLC6A19
 KEGG 10 / 103 4.1× 1.59e-4 3.25e-3 ✓ sig.
Carnitine metabolism
RXRA, CPT1B, PRKAA2, SLC22A5
 Reactome 4 / 14 12.1× 2.54e-4 4.70e-3 ✓ sig.
Laminin interactions
LAMA2, LAMB1, COL4A4, COL18A1, LAMA5
 Reactome 5 / 28 7.6× 4.49e-4 7.32e-3 ✓ sig.
Defective ACTH causes Obesity and Pro-opiomelanocortinin deficiency (POMCD)
MC2R, POMC
 Reactome 2 / 2 42.3× 5.57e-4 8.67e-3 ✓ sig.
Integrin cell surface interactions
COL5A1, COL2A1, COL4A4, COL9A1, FBN1, TNC, COL18A1, KDR
 Reactome 8 / 81 4.2× 6.39e-4 9.66e-3 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
BMP4, IL6, LAMB1, APOE, FBN1, IGF1, MMP2, TNC, FUCA2, PCSK9
 Reactome 10 / 125 3.4× 7.56e-4 1.10e-2 ✓ sig.
PI3K-Akt signaling pathway
GNB3, IL6, JAK2, LAMA2, LAMB1, NTF4, RXRA, GNGT2, COL2A1, COL4A4, COL9A1, HGF
 KEGG 19 / 361 2.2× 9.60e-4 1.32e-2 ✓ sig.
The canonical retinoid cycle in rods (twilight vision)
RDH5, LRAT, RLBP1, RPE65
 Reactome 4 / 20 8.5× 1.10e-3 1.46e-2 ✓ sig.
ECM-receptor interaction
LAMA2, LAMB1, AGRN, COL2A1, COL4A4, COL9A1, TNC, LAMA5
 KEGG 8 / 89 3.8× 1.19e-3 1.55e-2 ✓ sig.
ECM proteoglycans
COL5A1, AGRN, COL2A1, COL9A1, TNC, BCAN
 Reactome 6 / 51 5.0× 1.22e-3 1.58e-2 ✓ sig.
NCAM1 interactions
COL5A1, COL2A1, COL4A4, COL9A1
 Reactome 4 / 21 8.1× 1.33e-3 1.68e-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 ⇵
visual perception
EFEMP1, GJD2, RDH5, RGR, TYR, LRAT, RLBP1, RPE65, IRX5, RORB, ARR3, CACNA1F
 GO:0007601 20 / 215 6.1× 1.15e-10 3.25e-8 ✓ sig.
camera-type eye development
BMP4, EFEMP1, PRSS56, RPGRIP1L, RPE65, CHD7, FBN1, FBN2, SLC25A25
 GO:0043010 9 / 74 8.0× 1.78e-6 1.31e-4 ✓ sig.
skeletal system morphogenesis
ANKRD11, SGPL1, COL11A1, COL2A1, MMP2, LAMA5, HOXB8
 GO:0048705 7 / 45 10.2× 4.81e-6 2.91e-4 ✓ sig.
neuron projection development
IL6, LAMB1, MAP2, WNT7B, APOE, BLOC1S3, RASGRF1, TNC, VPS13B, EPHA8, FLRT3, PTPRZ1
 GO:0031175 12 / 161 4.9× 6.70e-6 3.79e-4 ✓ sig.
head development
RPGRIP1L, CHD7, SSBP3, FLRT3, PGAP1
 GO:0060322 5 / 21 15.7× 1.30e-5 6.43e-4 ✓ sig.
embryonic eye morphogenesis
EFEMP1, RARB, FBN1, FBN2
 GO:0048048 4 / 11 23.9× 1.58e-5 7.51e-4 ✓ sig.
central nervous system development
DSCAM, CHD7, DMBX1, DSCAML1, NOG, COL2A1, VPS13B, BCAN, NRCAM, PTPRZ1, SNTG2
 GO:0007417 11 / 158 4.6× 3.07e-5 1.24e-3 ✓ sig.
positive regulation of integrin-mediated signaling pathway
LAMA2, LAMB1, FLNA, LOXL3
 GO:2001046 4 / 13 20.2× 3.35e-5 1.33e-3 ✓ sig.
heart morphogenesis
BMP4, COL5A1, CHD7, BMP2, COL11A1, COL2A1, PTCH1
 GO:0003007 7 / 61 7.6× 3.76e-5 1.45e-3 ✓ sig.
nervous system development
DSCAM, GDPD5, NAV3, RBFOX1, RXRA, TCF4, LRP2, AGRN, DSCAML1, MARK4, NEUROD2, NOG
 GO:0007399 24 / 631 2.5× 3.76e-5 1.45e-3 ✓ sig.
lung development
BMP4, CCBE1, WNT7B, EP300, FBN1, IGF1, LOXL3, KDR, LAMA5
 GO:0030324 9 / 108 5.5× 4.01e-5 1.52e-3 ✓ sig.
positive regulation of cholesterol efflux
ABCA1, RXRA, APOE, PTCH1, NFKB1
 GO:0010875 5 / 27 12.2× 4.80e-5 1.74e-3 ✓ sig.
positive regulation of neuron differentiation
BMP4, GDPD5, PCP4, TCF4, NEUROD2, VWC2, BMP2, NRCAM
 GO:0045666 8 / 87 6.1× 5.33e-5 1.89e-3 ✓ sig.
clustering of voltage-gated sodium channels
AGRN, SCLT1, NRCAM
 GO:0045162 3 / 6 32.9× 6.72e-5 2.24e-3 ✓ sig.
limb morphogenesis
RPGRIP1L, NFIA, COL2A1, PTCH1, FBN2
 GO:0035108 5 / 31 10.6× 9.62e-5 2.94e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Eye disease Hyperopia 0.061 10 4.49e-11 4.89e-10 ✓ sig.
Eye disease Myopia 0.046 10 8.03e-9 7.03e-8 ✓ sig.
Hyperopia Myopia 0.039 8 3.91e-7 2.60e-6 ✓ sig.
Bone marrow failure and diabetes mellitus syndrome Myopia 0.007 1 8.64e-3 9.97e-3 ✓ sig.
cardiomyopathy, dilated, 2j Myopia 0.007 1 8.64e-3 9.97e-3 ✓ sig.
Myopia neurodevelopmental disorder with or without seizures and gait abnormalities 0.007 1 8.64e-3 9.97e-3 ✓ sig.
Hyperopia Trichotillomania 0.012 1 1.02e-2 1.16e-2 ✓ sig.