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 456

6 diseases · 11 shared-gene connections
6 Diseases
5 Unique genes
0.327 Avg. similarity score
Mitochondrial complex v (atp synthase) deficiency, nuclear type 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 ⇵
Mitochondrial complex v (atp synthase) deficiency, nuclear type 5 5 2
Intrauterine growth restriction 4 4 4
Mitochondrial complex v (atp synthase) deficiency, nuclear type 2 4 4 1
Mitochondrial encephalocardiomyopathy 4 4 1
Oligohydramnios 4 4 1
Mitochondrial complex v (atp synthase) deficiency, nuclear type 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TMEM70 5 / 6 Intrauterine growth restriction, Mitochondrial complex v (atp synthase) deficiency, nuclear type, Mitochondrial complex v (atp synthase) deficiency, nuclear type 2, Mitochondrial encephalocardiomyopathy and 1 more
ATPAF2 2 / 6 Mitochondrial complex v (atp synthase) deficiency, nuclear type, Mitochondrial complex v (atp synthase) deficiency, nuclear type 1
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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Chromatin modifying enzymes
PADI6
 Reactome 1 / 20 120× 8.30e-3 5.06e-2
Other types of O-glycan biosynthesis
PLOD3
 KEGG 1 / 47 51.1× 1.94e-2 8.43e-2
Lysine degradation
PLOD3
 KEGG 1 / 63 38.1× 2.60e-2 9.96e-2
Collagen biosynthesis and modifying enzymes
PLOD3
 Reactome 1 / 67 35.9× 2.76e-2 1.03e-1
NOD-like receptor signaling pathway
NLRP7
 KEGG 1 / 187 12.8× 7.55e-2 1.84e-1
Metabolic pathways
PLOD3
 KEGG 1 / 1,563 1.5× 5.02e-1 6.20e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
mitochondrial proton-transporting ATP synthase complex assembly
TMEM70, ATPAF2
 GO:0033615 2 / 8 934× 1.60e-6 1.27e-4 ✓ sig.
regulation of translation by machinery localization
PADI6
 GO:0043143 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
proton-transporting ATP synthase complex assembly
ATPAF2
 GO:0043461 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
hydroxylysine biosynthetic process
PLOD3
 GO:0046947 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
intracellular protein localization
PADI6, PLOD3
 GO:0008104 2 / 194 38.5× 1.05e-3 1.51e-2 ✓ sig.
basement membrane assembly
PLOD3
 GO:0070831 1 / 5 747× 1.34e-3 1.71e-2 ✓ sig.
protein storage
PADI6
 GO:0140089 1 / 5 747× 1.34e-3 1.71e-2 ✓ sig.
cytoplasm organization
PADI6
 GO:0007028 1 / 6 623× 1.60e-3 1.88e-2 ✓ sig.
in utero embryonic development
PADI6, PLOD3
 GO:0001701 2 / 252 29.7× 1.76e-3 1.99e-2 ✓ sig.
epidermis morphogenesis
PLOD3
 GO:0048730 1 / 7 534× 1.87e-3 2.05e-2 ✓ sig.
peptidyl-lysine hydroxylation
PLOD3
 GO:0017185 1 / 7 534× 1.87e-3 2.05e-2 ✓ sig.
epigenetic programming in the zygotic pronuclei
PADI6
 GO:0044725 1 / 9 415× 2.41e-3 2.32e-2 ✓ sig.
embryonic cleavage
PADI6
 GO:0040016 1 / 9 415× 2.41e-3 2.32e-2 ✓ sig.
endothelial cell morphogenesis
PLOD3
 GO:0001886 1 / 15 249× 4.01e-3 3.01e-2 ✓ sig.
negative regulation of protein processing
NLRP7
 GO:0010955 1 / 15 249× 4.01e-3 3.01e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Mitochondrial complex v (atp synthase) deficiency, nuclear type 2 Mitochondrial encephalocardiomyopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mitochondrial complex v (atp synthase) deficiency, nuclear type 2 Oligohydramnios 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mitochondrial encephalocardiomyopathy Oligohydramnios 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Mitochondrial complex v (atp synthase) deficiency, nuclear type Mitochondrial encephalocardiomyopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mitochondrial complex v (atp synthase) deficiency, nuclear type Oligohydramnios 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mitochondrial complex v (atp synthase) deficiency, nuclear type Mitochondrial complex v (atp synthase) deficiency, nuclear type 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mitochondrial complex v (atp synthase) deficiency, nuclear type Mitochondrial complex v (atp synthase) deficiency, nuclear type 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intrauterine growth restriction Mitochondrial encephalocardiomyopathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Intrauterine growth restriction Mitochondrial complex v (atp synthase) deficiency, nuclear type 2 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Intrauterine growth restriction Oligohydramnios 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Intrauterine growth restriction Mitochondrial complex v (atp synthase) deficiency, nuclear type 0.167 1 5.16e-4 9.13e-4 ✓ sig.