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 168

9 diseases · 16 shared-gene connections
9 Diseases
13 Unique genes
0.259 Avg. similarity score
Carbamoyl phosphate synthetase deficiency Most-connected disease (5 links)
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Disease Searched: Hypoplastic anemia 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 ⇵
Carbamoyl phosphate synthetase deficiency 5 5 2
Congenital facial anomaly 5 5 3
Congenital hypoplastic anemia 5 5 2
Hypoplastic anemia 5 5 2
developmental and epileptic encephalopathy, 50 5 5 1
Spherocytosis 4 4 10
Congenital hyperammonemia 1 1 1
Thauvin-robinet-faivre syndrome 1 1 1
hereditary spherocytosis 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CAD 6 / 9 Carbamoyl phosphate synthetase deficiency, Congenital facial anomaly, Congenital hypoplastic anemia, developmental and epileptic encephalopathy, 50 and 2 more
UMPS 3 / 9 Congenital hypoplastic anemia, Hypoplastic anemia, Spherocytosis
ANK1 2 / 9 hereditary spherocytosis, Spherocytosis
CPS1 2 / 9 Carbamoyl phosphate synthetase deficiency, Congenital hyperammonemia
FIBP 2 / 9 Congenital facial anomaly, Thauvin-robinet-faivre 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 ⇵
Pyrimidine biosynthesis
CAD, UMPS, DHODH
 Reactome 3 / 3 924× 9.91e-10 1.16e-7 ✓ sig.
Interaction between L1 and Ankyrins
SPTB, SPTA1, ANK1
 Reactome 3 / 13 213× 2.82e-7 1.73e-5 ✓ sig.
Pyrimidine metabolism
CAD, UMPS, DHODH
 KEGG 3 / 58 47.8× 2.95e-5 8.66e-4 ✓ sig.
COPI-mediated anterograde transport
SPTB, SPTA1, ANK1
 Reactome 3 / 101 27.4× 1.55e-4 3.28e-3 ✓ sig.
NCAM signaling for neurite out-growth
SPTB, SPTA1
 Reactome 2 / 20 92.4× 2.03e-4 4.07e-3 ✓ sig.
Arginine biosynthesis
CAD, CPS1
 KEGG 2 / 23 80.3× 2.70e-4 5.08e-3 ✓ sig.
Biosynthesis of cofactors
CAD, UMPS, DHODH
 KEGG 3 / 154 18.0× 5.38e-4 8.74e-3 ✓ sig.
Alanine, aspartate and glutamate metabolism
CAD, CPS1
 KEGG 2 / 37 49.9× 7.05e-4 1.08e-2 ✓ sig.
Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA)
SLC4A1
 Reactome 1 / 1 924× 1.08e-3 1.50e-2 ✓ sig.
Neurofascin interactions
ANK1
 Reactome 1 / 4 231× 4.32e-3 4.10e-2 ✓ sig.
RAF/MAP kinase cascade
SPTB, SPTA1
 Reactome 2 / 124 14.9× 7.66e-3 5.98e-2
HuR (ELAVL1) binds and stabilizes mRNA
NUP214
 Reactome 1 / 8 115× 8.63e-3 6.46e-2
Erythrocytes take up oxygen and release carbon dioxide
SLC4A1
 Reactome 1 / 9 103× 9.70e-3 6.96e-2
Urea cycle
CPS1
 Reactome 1 / 10 92.4× 1.08e-2 7.43e-2
Bicarbonate transporters
SLC4A1
 Reactome 1 / 10 92.4× 1.08e-2 7.43e-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, DHODH
 GO:0006207 4 / 6 958× 2.11e-12 9.12e-10 ✓ sig.
'de novo' UMP biosynthetic process
CAD, UMPS, DHODH
 GO:0044205 3 / 3 1,437× 2.63e-10 6.90e-8 ✓ sig.
UDP biosynthetic process
CAD, UMPS, DHODH
 GO:0006225 3 / 5 862× 2.63e-9 5.28e-7 ✓ sig.
pyrimidine nucleotide biosynthetic process
CAD, UMPS, DHODH
 GO:0006221 3 / 9 479× 2.20e-8 3.41e-6 ✓ sig.
citrulline biosynthetic process
CAD, CPS1
 GO:0019240 2 / 4 719× 2.68e-6 1.88e-4 ✓ sig.
response to amine
CAD, CPS1
 GO:0014075 2 / 10 287× 2.00e-5 9.30e-4 ✓ sig.
glutamine metabolic process
CAD, CPS1
 GO:0006541 2 / 15 192× 4.67e-5 1.77e-3 ✓ sig.
actin filament capping
SPTB, SPTA1
 GO:0051693 2 / 19 151× 7.59e-5 2.55e-3 ✓ sig.
response to starvation
CAD, CPS1
 GO:0042594 2 / 37 77.7× 2.93e-4 6.84e-3 ✓ sig.
carbamoyl phosphate biosynthetic process
CPS1
 GO:0070409 1 / 1 1,437× 6.96e-4 1.23e-2 ✓ sig.
pH elevation
SLC4A1
 GO:0045852 1 / 1 1,437× 6.96e-4 1.23e-2 ✓ sig.
response to oleic acid
CPS1
 GO:0034201 1 / 2 719× 1.39e-3 1.90e-2 ✓ sig.
monoatomic anion homeostasis
CPS1
 GO:0055081 1 / 2 719× 1.39e-3 1.90e-2 ✓ sig.
pyrimidine-containing compound biosynthetic process
CAD
 GO:0072528 1 / 2 719× 1.39e-3 1.90e-2 ✓ sig.
liver development
CAD, CPS1
 GO:0001889 2 / 87 33.0× 1.62e-3 2.07e-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 6.82e-8 ✓ sig.
Congenital hypoplastic anemia Spherocytosis 0.182 2 3.80e-7 2.39e-6 ✓ sig.
Hypoplastic anemia Spherocytosis 0.182 2 3.80e-7 2.39e-6 ✓ sig.
Carbamoyl phosphate synthetase deficiency Congenital hyperammonemia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency developmental and epileptic encephalopathy, 50 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital hypoplastic anemia developmental and epileptic encephalopathy, 50 0.333 1 1.30e-4 3.93e-4 ✓ sig.
developmental and epileptic encephalopathy, 50 Hypoplastic anemia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital facial anomaly Thauvin-robinet-faivre syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital facial anomaly developmental and epileptic encephalopathy, 50 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Hypoplastic anemia 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Congenital hypoplastic anemia 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Carbamoyl phosphate synthetase deficiency Congenital facial anomaly 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Congenital facial anomaly Hypoplastic anemia 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Congenital facial anomaly Congenital hypoplastic anemia 0.200 1 3.90e-4 8.67e-4 ✓ sig.
developmental and epileptic encephalopathy, 50 Spherocytosis 0.091 1 6.49e-4 1.24e-3 ✓ sig.
hereditary spherocytosis Spherocytosis 0.091 1 6.49e-4 1.24e-3 ✓ sig.