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 630

5 diseases · 5 shared-gene connections
5 Diseases
4 Unique genes
0.273 Avg. similarity score
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome Most-connected disease (3 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 ⇵
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 3 3 2
Lipoyltransferase deficiency 3 3 3
Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities 2 2 1
Leigh syndrome with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase 1 1 1
Progressive childhood encephalopathy and golgi dysfunction 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LIPT2 3 / 5 Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome, Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities, Lipoyltransferase deficiency
LIPT1 2 / 5 Leigh syndrome with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase, Lipoyltransferase deficiency
TRAPPC12 2 / 5 Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome, Progressive childhood encephalopathy and golgi dysfunction
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 ⇵
Lipoic acid metabolism
LIPT2, LIPT1
 KEGG 2 / 19 316× 1.42e-5 3.90e-4 ✓ sig.
Glyoxylate metabolism and glycine degradation
LIPT2, LIPT1
 Reactome 2 / 28 214× 3.14e-5 7.52e-4 ✓ sig.
Biosynthesis of cofactors
LIPT2, LIPT1
 KEGG 2 / 154 39.0× 9.64e-4 1.10e-2 ✓ sig.
RAB GEFs exchange GTP for GDP on RABs
TRAPPC12
 Reactome 1 / 90 33.4× 2.96e-2 1.07e-1
Metabolic pathways
LIPT2, LIPT1
 KEGG 2 / 1,563 3.8× 8.48e-2 1.96e-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 ⇵
protein lipoylation
LIPT2, LIPT1
 GO:0009249 2 / 5 1,869× 3.44e-7 3.56e-5 ✓ sig.
positive regulation of oxygen metabolic process
LIPT2
 GO:2000376 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
positive regulation of protein localization to kinetochore
TRAPPC12
 GO:1905342 1 / 2 2,336× 4.28e-4 8.53e-3 ✓ sig.
regulation of kinetochore assembly
TRAPPC12
 GO:0090234 1 / 3 1,557× 6.42e-4 1.11e-2 ✓ sig.
metaphase chromosome alignment
TRAPPC12
 GO:0051310 1 / 16 292× 3.42e-3 2.78e-2 ✓ sig.
vesicle tethering
TRAPPC12
 GO:0099022 1 / 16 292× 3.42e-3 2.78e-2 ✓ sig.
viral budding via host ESCRT complex
MITD1
 GO:0039702 1 / 23 203× 4.91e-3 3.31e-2 ✓ sig.
COPII vesicle coating
TRAPPC12
 GO:0048208 1 / 23 203× 4.91e-3 3.31e-2 ✓ sig.
midbody abscission
MITD1
 GO:0061952 1 / 24 195× 5.13e-3 3.37e-2 ✓ sig.
multivesicular body sorting pathway
MITD1
 GO:0071985 1 / 24 195× 5.13e-3 3.37e-2 ✓ sig.
negative regulation of protein binding
MITD1
 GO:0032091 1 / 26 180× 5.55e-3 3.51e-2 ✓ sig.
mitotic cytokinesis
MITD1
 GO:0000281 1 / 68 68.7× 1.45e-2 5.55e-2
protein modification process
LIPT1
 GO:0036211 1 / 84 55.6× 1.79e-2 6.13e-2
Golgi organization
TRAPPC12
 GO:0007030 1 / 128 36.5× 2.71e-2 7.68e-2
endoplasmic reticulum to Golgi vesicle-mediated transport
TRAPPC12
 GO:0006888 1 / 133 35.1× 2.82e-2 7.83e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome Progressive childhood encephalopathy and golgi dysfunction 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities Lipoyltransferase deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Leigh syndrome with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase Lipoyltransferase deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome Lipoyltransferase deficiency 0.200 1 3.87e-4 7.33e-4 ✓ sig.