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 372

7 diseases · 8 shared-gene connections
7 Diseases
79 Unique genes
0.054 Avg. similarity score
Nonimmune hydrops fetalis Most-connected disease (6 links)
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Disease Searched: Nonimmune hydrops fetalis 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 ⇵
Nonimmune hydrops fetalis 6 6 48
Hydrops fetalis 3 3 33
Lymphatic malformation 2 2 13
Mucopolysaccharidosis type 7 2 2 1
Congenital malrotation of intestine 1 1 1
Desmosterolosis 1 1 1
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CALCRL 3 / 7 Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis
EPHB4 3 / 7 Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis
GUSB 3 / 7 Hydrops fetalis, Mucopolysaccharidosis type 7, Nonimmune hydrops fetalis
PIEZO1 3 / 7 Hydrops fetalis, Lymphatic malformation, Nonimmune hydrops fetalis
ANGPT2 2 / 7 Lymphatic malformation, Nonimmune hydrops fetalis
ASAH1 2 / 7 Hydrops fetalis, Nonimmune hydrops fetalis
CELSR1 2 / 7 Hydrops fetalis, Lymphatic malformation
CHRNA1 2 / 7 Hydrops fetalis, Nonimmune hydrops fetalis
DHCR24 2 / 7 Desmosterolosis, Nonimmune hydrops fetalis
FLT4 2 / 7 Lymphatic malformation, Nonimmune hydrops fetalis
GALNT14 2 / 7 Congenital malrotation of intestine, Nonimmune hydrops fetalis
MDFIC 2 / 7 Hydrops fetalis, Lymphatic malformation
MOCS3 2 / 7 Nonimmune hydrops fetalis, Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2
SERPINA11 2 / 7 Hydrops fetalis, Nonimmune hydrops fetalis
THSD1 2 / 7 Lymphatic malformation, Nonimmune hydrops fetalis
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 ⇵
Tie2 Signaling
ANGPT2, HRAS, KRAS, PTPN11
 Reactome 4 / 18 33.8× 4.95e-6 1.63e-4 ✓ sig.
EPHB-mediated forward signaling
RASA1, EPHB4, HRAS, ROCK2, CDC42
 Reactome 5 / 39 19.5× 5.24e-6 1.71e-4 ✓ sig.
Ras signaling pathway
RASA1, ANGPT2, FLT4, HRAS, KRAS, PTPN11, SHOC2, VEGFC, CDC42
 KEGG 9 / 237 5.8× 2.41e-5 6.09e-4 ✓ sig.
Axon guidance
L1CAM, RASA1, EPHB4, HRAS, KRAS, PTPN11, ROCK2, CDC42
 KEGG 8 / 183 6.6× 2.59e-5 6.44e-4 ✓ sig.
Downstream signal transduction
RASA1, HRAS, KRAS, PTPN11
 Reactome 4 / 29 21.0× 3.63e-5 8.47e-4 ✓ sig.
PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases
RASA1, HRAS, KRAS
 Reactome 3 / 14 32.6× 9.46e-5 1.82e-3 ✓ sig.
VEGFR2 mediated cell proliferation
RASA1, HRAS, KRAS
 Reactome 3 / 14 32.6× 9.46e-5 1.82e-3 ✓ sig.
Defective NEU1 causes sialidosis
CTSA, NEU1
 Reactome 2 / 3 101× 1.28e-4 2.30e-3 ✓ sig.
RAS GTPase cycle mutants
HRAS, KRAS
 Reactome 2 / 3 101× 1.28e-4 2.30e-3 ✓ sig.
FRS-mediated FGFR3 signaling
HRAS, KRAS, PTPN11
 Reactome 3 / 20 22.8× 2.88e-4 4.37e-3 ✓ sig.
NCAM signaling for neurite out-growth
HRAS, KRAS, SPTA1
 Reactome 3 / 20 22.8× 2.88e-4 4.37e-3 ✓ sig.
FRS-mediated FGFR4 signaling
HRAS, KRAS, PTPN11
 Reactome 3 / 22 20.7× 3.86e-4 5.46e-3 ✓ sig.
Activation of RAS in B cells
HRAS, KRAS
 Reactome 2 / 5 60.8× 4.22e-4 5.86e-3 ✓ sig.
FRS-mediated FGFR1 signaling
HRAS, KRAS, PTPN11
 Reactome 3 / 23 19.8× 4.41e-4 6.06e-3 ✓ sig.
FRS-mediated FGFR2 signaling
HRAS, KRAS, PTPN11
 Reactome 3 / 25 18.2× 5.68e-4 7.37e-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 ⇵
lymphangiogenesis
CCBE1, FLT4, FOXC2
 GO:0001946 3 / 14 50.7× 2.56e-5 1.11e-3 ✓ sig.
angiogenesis
CCBE1, RASA1, ANGPT2, CALCRL, EPHB4, FLT4, VEGFC, TIE1
 GO:0001525 8 / 284 6.7× 2.64e-5 1.14e-3 ✓ sig.
lymph vessel development
CCBE1, FLT4, FOXC2
 GO:0001945 3 / 15 47.3× 3.19e-5 1.31e-3 ✓ sig.
establishment of body hair planar orientation
CELSR1, FZD6
 GO:0048105 2 / 4 118× 1.05e-4 3.22e-3 ✓ sig.
positive regulation of lymphangiogenesis
CCBE1, VEGFC
 GO:1901492 2 / 4 118× 1.05e-4 3.22e-3 ✓ sig.
vascular endothelial growth factor receptor signaling pathway
FLT4, FOXC2, VEGFC
 GO:0048010 3 / 31 22.9× 3.00e-4 6.79e-3 ✓ sig.
Ras protein signal transduction
DHCR24, HRAS, KRAS, RIT1
 GO:0007265 4 / 79 12.0× 3.49e-4 7.48e-3 ✓ sig.
Wnt signaling pathway, planar cell polarity pathway
CELSR1, FZD6, CDC42
 GO:0060071 3 / 34 20.9× 3.96e-4 8.12e-3 ✓ sig.
blood vessel morphogenesis
RASA1, ANGPT2, FLT4
 GO:0048514 3 / 34 20.9× 3.96e-4 8.12e-3 ✓ sig.
host-mediated perturbation of viral process
ROCK2, CDC42
 GO:0044788 2 / 8 59.1× 4.86e-4 9.30e-3 ✓ sig.
sprouting angiogenesis
CCBE1, FLT4, VEGFC
 GO:0002040 3 / 37 19.2× 5.09e-4 9.61e-3 ✓ sig.
release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
RYR1, RYR3
 GO:0014808 2 / 9 52.6× 6.23e-4 1.11e-2 ✓ sig.
cellular response to caffeine
RYR1, RYR3
 GO:0071313 2 / 11 43.0× 9.47e-4 1.42e-2 ✓ sig.
regulation of actin cytoskeleton organization
CELSR1, HRAS, ROCK2, CDC42
 GO:0032956 4 / 104 9.1× 9.88e-4 1.45e-2 ✓ sig.
positive regulation of protein secretion
MYO18A, MYOM1, VEGFC
 GO:0050714 3 / 49 14.5× 1.16e-3 1.59e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Lymphatic malformation Nonimmune hydrops fetalis 0.109 6 9.47e-13 1.02e-11 ✓ sig.
Hydrops fetalis Nonimmune hydrops fetalis 0.095 7 5.98e-12 6.13e-11 ✓ sig.
Hydrops fetalis Lymphatic malformation 0.119 5 4.07e-11 3.94e-10 ✓ sig.
Hydrops fetalis Mucopolysaccharidosis type 7 0.029 1 2.13e-3 2.85e-3 ✓ sig.
Congenital malrotation of intestine Nonimmune hydrops fetalis 0.021 1 3.03e-3 3.86e-3 ✓ sig.
Desmosterolosis Nonimmune hydrops fetalis 0.021 1 3.03e-3 3.86e-3 ✓ sig.
Mucopolysaccharidosis type 7 Nonimmune hydrops fetalis 0.021 1 3.03e-3 3.86e-3 ✓ sig.
Nonimmune hydrops fetalis Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B2 0.021 1 3.03e-3 3.86e-3 ✓ sig.