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Cluster 471

6 diseases · 14 shared-gene connections

6 Diseases

12 Unique genes

0.312 Avg. similarity score

Congenital heart defects, multiple types, 7 Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

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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.

Congenital heart defects, multiple types, 7 Lymphatic malformation 1 Lymphedema, hereditary, ia Milroy disease Capillary infantile hemangioma Fetal hydrops

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital heart defects, multiple types, 7	5	5	1
Lymphatic malformation 1	5	5	1
Lymphedema, hereditary, ia	5	5	1
Milroy disease	5	5	1
Capillary infantile hemangioma	4	4	3
Fetal hydrops	4	4	10

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

Gene ⇵	Member diseases ⇵	Linked diseases
FLT4	6 / 6	Capillary infantile hemangioma, Congenital heart defects, multiple types, 7, Fetal hydrops, Lymphatic malformation 1 and 2 more

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 ⇵
VEGF binds to VEGFR leading to receptor dimerization FLT4, KDR	Reactome	2 / 8	250×	2.55e-5	6.38e-4 ✓ sig.
Lysosome NEU1, LIPA, ASAH1	KEGG	3 / 133	22.6×	2.72e-4	4.18e-3 ✓ sig.
Glycosphingolipid metabolism NEU1, ASAH1	Reactome	2 / 46	43.5×	9.24e-4	1.07e-2 ✓ sig.
Defective AHCY causes Hypermethioninemia with S-adenosylhomocysteine hydrolase deficiency (HMAHCHD) AHCY	Reactome	1 / 1	1,001×	9.99e-4	1.13e-2 ✓ sig.
Sphingolipid metabolism NEU1, ASAH1	KEGG	2 / 54	37.1×	1.27e-3	1.36e-2 ✓ sig.
Defective NEU1 causes sialidosis NEU1	Reactome	1 / 3	334×	2.99e-3	2.54e-2 ✓ sig.
Neurophilin interactions with VEGF and VEGFR KDR	Reactome	1 / 4	250×	3.99e-3	3.12e-2 ✓ sig.
Signaling by membrane-tethered fusions of PDGFRA or PDGFRB KDR	Reactome	1 / 5	200×	4.99e-3	3.64e-2 ✓ sig.
Sulfur amino acid metabolism AHCY	Reactome	1 / 6	167×	5.98e-3	4.10e-2 ✓ sig.
RUNX1 regulates transcription of genes involved in WNT signaling FOXP3	Reactome	1 / 6	167×	5.98e-3	4.10e-2 ✓ sig.
RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) FOXP3	Reactome	1 / 10	100×	9.95e-3	5.67e-2
Uptake and function of anthrax toxins ANTXR1	Reactome	1 / 13	77.0×	1.29e-2	6.62e-2
Methylation AHCY	Reactome	1 / 14	71.5×	1.39e-2	6.94e-2
VEGFR2 mediated cell proliferation KDR	Reactome	1 / 14	71.5×	1.39e-2	6.94e-2
Focal adhesion FLT4, KDR	KEGG	2 / 203	9.9×	1.68e-2	7.75e-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 ⇵
lymph vessel development FLT4, KDR, CCBE1, FOXC2	GO:0001945	4 / 15	415×	1.33e-10	3.93e-8 ✓ sig.
positive regulation of endothelial cell migration FLT4, KDR, CCBE1, FOXC2	GO:0010595	4 / 66	94.4×	6.88e-8	9.31e-6 ✓ sig.
lymphangiogenesis FLT4, CCBE1, FOXC2	GO:0001946	3 / 14	334×	7.33e-8	9.83e-6 ✓ sig.
vascular endothelial growth factor receptor signaling pathway FLT4, KDR, FOXC2	GO:0048010	3 / 31	151×	9.00e-7	7.87e-5 ✓ sig.
response to rapamycin LIPA, FOXP3	GO:1901355	2 / 4	779×	2.27e-6	1.68e-4 ✓ sig.
blood vessel endothelial cell differentiation KDR, LIPA	GO:0060837	2 / 5	623×	3.78e-6	2.53e-4 ✓ sig.
lung development KDR, LIPA, CCBE1	GO:0030324	3 / 108	43.3×	3.98e-5	1.55e-3 ✓ sig.
respiratory system process FLT4, CCBE1	GO:0003016	2 / 19	164×	6.43e-5	2.23e-3 ✓ sig.
vascular endothelial growth factor signaling pathway FLT4, KDR	GO:0038084	2 / 19	164×	6.43e-5	2.23e-3 ✓ sig.
respiratory gaseous exchange by respiratory system FLT4, CCBE1	GO:0007585	2 / 31	100×	1.74e-4	4.60e-3 ✓ sig.
positive regulation of vascular endothelial growth factor production FLT4, CCBE1	GO:0010575	2 / 32	97.3×	1.86e-4	4.82e-3 ✓ sig.
cellular response to vascular endothelial growth factor stimulus FLT4, KDR	GO:0035924	2 / 33	94.4×	1.97e-4	5.03e-3 ✓ sig.
vasculature development FLT4, KDR	GO:0001944	2 / 33	94.4×	1.97e-4	5.03e-3 ✓ sig.
branching involved in blood vessel morphogenesis KDR, FOXC2	GO:0001569	2 / 33	94.4×	1.97e-4	5.03e-3 ✓ sig.
positive regulation of cell migration involved in sprouting angiogenesis KDR, FOXC2	GO:0090050	2 / 37	84.2×	2.49e-4	5.92e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Congenital heart defects, multiple types, 7	Lymphatic malformation 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital heart defects, multiple types, 7	Milroy disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital heart defects, multiple types, 7	Lymphedema, hereditary, ia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Lymphatic malformation 1	Milroy disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Lymphatic malformation 1	Lymphedema, hereditary, ia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Lymphedema, hereditary, ia	Milroy disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Capillary infantile hemangioma	Congenital heart defects, multiple types, 7	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Capillary infantile hemangioma	Lymphatic malformation 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Capillary infantile hemangioma	Milroy disease	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Capillary infantile hemangioma	Lymphedema, hereditary, ia	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Congenital heart defects, multiple types, 7	Fetal hydrops	0.091	1	6.46e-4	1.09e-3 ✓ sig.
Fetal hydrops	Lymphatic malformation 1	0.091	1	6.46e-4	1.09e-3 ✓ sig.
Fetal hydrops	Lymphedema, hereditary, ia	0.091	1	6.46e-4	1.09e-3 ✓ sig.
Fetal hydrops	Milroy disease	0.091	1	6.46e-4	1.09e-3 ✓ sig.

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