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 347

6 diseases · 11 shared-gene connections
6 Diseases
5 Unique genes
0.297 Avg. similarity score
Congenital facial anomaly 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 ⇵
Congenital facial anomaly 5 5 3
Carbamoyl phosphate synthetase deficiency 4 4 2
Congenital hypoplastic anemia 4 4 2
Hypoplastic anemia 4 4 2
developmental and epileptic encephalopathy, 50 4 4 1
Thauvin-robinet-faivre syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CAD 5 / 6 Carbamoyl phosphate synthetase deficiency, Congenital facial anomaly, Congenital hypoplastic anemia, developmental and epileptic encephalopathy, 50 and 1 more
FIBP 2 / 6 Congenital facial anomaly, Thauvin-robinet-faivre syndrome
UMPS 2 / 6 Congenital hypoplastic anemia, Hypoplastic anemia
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 ⇵
Pyrimidine biosynthesis
CAD, UMPS
 Reactome 2 / 3 1,601× 4.16e-7 2.28e-5 ✓ sig.
Arginine biosynthesis
CAD, CPS1
 KEGG 2 / 23 209× 3.50e-5 9.50e-4 ✓ sig.
Alanine, aspartate and glutamate metabolism
CAD, CPS1
 KEGG 2 / 37 130× 9.18e-5 2.09e-3 ✓ sig.
Pyrimidine metabolism
CAD, UMPS
 KEGG 2 / 58 82.8× 2.27e-4 4.33e-3 ✓ sig.
Biosynthesis of cofactors
CAD, UMPS
 KEGG 2 / 154 31.2× 1.59e-3 1.93e-2 ✓ sig.
HuR (ELAVL1) binds and stabilizes mRNA
NUP214
 Reactome 1 / 8 300× 3.33e-3 3.31e-2 ✓ sig.
Urea cycle
CPS1
 Reactome 1 / 10 240× 4.16e-3 3.87e-2 ✓ sig.
Nitrogen metabolism
CPS1
 KEGG 1 / 17 141× 7.06e-3 5.49e-2
Transport of Ribonucleoproteins into the Host Nucleus
NUP214
 Reactome 1 / 31 77.5× 1.28e-2 7.92e-2
NEP/NS2 Interacts with the Cellular Export Machinery
NUP214
 Reactome 1 / 31 77.5× 1.28e-2 7.92e-2
Regulation of Glucokinase by Glucokinase Regulatory Protein
NUP214
 Reactome 1 / 31 77.5× 1.28e-2 7.92e-2
Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)
NUP214
 Reactome 1 / 31 77.5× 1.28e-2 7.92e-2
Vpr-mediated nuclear import of PICs
NUP214
 Reactome 1 / 33 72.8× 1.37e-2 8.23e-2
Transport of the SLBP independent Mature mRNA
NUP214
 Reactome 1 / 34 70.6× 1.41e-2 8.38e-2
SUMOylation of SUMOylation proteins
NUP214
 Reactome 1 / 34 70.6× 1.41e-2 8.38e-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 ⇵
'de novo' pyrimidine nucleobase biosynthetic process
CAD, UMPS, CPS1
 GO:0006207 3 / 6 1,869× 1.84e-10 4.96e-8 ✓ sig.
'de novo' UMP biosynthetic process
CAD, UMPS
 GO:0044205 2 / 3 2,492× 1.72e-7 1.91e-5 ✓ sig.
citrulline biosynthetic process
CAD, CPS1
 GO:0019240 2 / 4 1,869× 3.44e-7 3.40e-5 ✓ sig.
UDP biosynthetic process
CAD, UMPS
 GO:0006225 2 / 5 1,495× 5.73e-7 5.25e-5 ✓ sig.
pyrimidine nucleotide biosynthetic process
CAD, UMPS
 GO:0006221 2 / 9 831× 2.06e-6 1.47e-4 ✓ sig.
response to amine
CAD, CPS1
 GO:0014075 2 / 10 747× 2.58e-6 1.76e-4 ✓ sig.
glutamine metabolic process
CAD, CPS1
 GO:0006541 2 / 15 498× 6.01e-6 3.47e-4 ✓ sig.
response to starvation
CAD, CPS1
 GO:0042594 2 / 37 202× 3.80e-5 1.46e-3 ✓ sig.
liver development
CAD, CPS1
 GO:0001889 2 / 87 85.9× 2.12e-4 5.27e-3 ✓ sig.
carbamoyl phosphate biosynthetic process
CPS1
 GO:0070409 1 / 1 3,737× 2.68e-4 6.20e-3 ✓ sig.
response to oleic acid
CPS1
 GO:0034201 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
monoatomic anion homeostasis
CPS1
 GO:0055081 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
pyrimidine-containing compound biosynthetic process
CAD
 GO:0072528 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
cellular response to oleic acid
CPS1
 GO:0071400 1 / 3 1,246× 8.03e-4 1.30e-2 ✓ sig.
UMP biosynthetic process
UMPS
 GO:0006222 1 / 3 1,246× 8.03e-4 1.30e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital hypoplastic anemia Hypoplastic anemia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Carbamoyl phosphate synthetase deficiency developmental and epileptic encephalopathy, 50 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital hypoplastic anemia developmental and epileptic encephalopathy, 50 0.333 1 1.30e-4 3.90e-4 ✓ sig.
developmental and epileptic encephalopathy, 50 Hypoplastic anemia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital facial anomaly Thauvin-robinet-faivre syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital facial anomaly developmental and epileptic encephalopathy, 50 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Hypoplastic anemia 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Congenital hypoplastic anemia 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital facial anomaly Hypoplastic anemia 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Congenital facial anomaly 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Congenital facial anomaly Congenital hypoplastic anemia 0.200 1 3.90e-4 8.52e-4 ✓ sig.