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 380

5 diseases · 8 shared-gene connections
5 Diseases
3 Unique genes
0.344 Avg. similarity score
Cerebral creatine deficiency syndrome Most-connected disease (4 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 ⇵
Cerebral creatine deficiency syndrome 4 4 3
Creatine deficiency 4 4 2
Creatine transporter deficiency 3 3 1
X-linked creatine transporter deficiency 3 3 1
Guanidinoacetate methyltransferase deficiency 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SLC6A8 4 / 5 Cerebral creatine deficiency syndrome, Creatine deficiency, Creatine transporter deficiency, X-linked creatine transporter deficiency
GAMT 3 / 5 Cerebral creatine deficiency syndrome, Creatine deficiency, Guanidinoacetate methyltransferase deficiency
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 ⇵
Creatine metabolism
GAMT, GATM, SLC6A8
 Reactome 3 / 11 1,092× 5.72e-10 6.80e-8 ✓ sig.
Glycine, serine and threonine metabolism
GAMT, GATM
 KEGG 2 / 40 200× 3.24e-5 8.90e-4 ✓ sig.
Arginine and proline metabolism
GAMT, GATM
 KEGG 2 / 50 160× 5.08e-5 1.30e-3 ✓ sig.
Metabolic pathways
GAMT, GATM
 KEGG 2 / 1,563 5.1× 4.64e-2 1.65e-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 ⇵
creatine metabolic process
GAMT, GATM, SLC6A8
 GO:0006600 3 / 4 4,672× 3.68e-12 1.48e-9 ✓ sig.
creatine biosynthetic process
GAMT, GATM
 GO:0006601 2 / 2 6,229× 1.72e-8 2.73e-6 ✓ sig.
muscle contraction
GAMT, SLC6A8
 GO:0006936 2 / 85 147× 6.12e-5 2.09e-3 ✓ sig.
muscle atrophy
GATM
 GO:0014889 1 / 2 3,115× 3.21e-4 7.03e-3 ✓ sig.
gamma-aminobutyric acid transport
SLC6A8
 GO:0015812 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
creatine transmembrane transport
SLC6A8
 GO:0015881 1 / 4 1,557× 6.42e-4 1.13e-2 ✓ sig.
regulation of multicellular organism growth
GAMT
 GO:0040014 1 / 26 240× 4.17e-3 3.34e-2 ✓ sig.
neurotransmitter transport
SLC6A8
 GO:0006836 1 / 57 109× 9.12e-3 4.89e-2 ✓ sig.
amino acid transport
SLC6A8
 GO:0006865 1 / 71 87.7× 1.14e-2 5.47e-2
learning or memory
GATM
 GO:0007611 1 / 72 86.5× 1.15e-2 5.51e-2
positive regulation of cold-induced thermogenesis
GATM
 GO:0120162 1 / 102 61.1× 1.63e-2 6.47e-2
animal organ morphogenesis
GAMT
 GO:0009887 1 / 130 47.9× 2.07e-2 7.31e-2
sodium ion transmembrane transport
SLC6A8
 GO:0035725 1 / 134 46.5× 2.14e-2 7.44e-2
sodium ion transport
SLC6A8
 GO:0006814 1 / 144 43.3× 2.29e-2 7.72e-2
methylation
GAMT
 GO:0032259 1 / 191 32.6× 3.04e-2 8.84e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cerebral creatine deficiency syndrome Creatine deficiency 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Creatine transporter deficiency X-linked creatine transporter deficiency 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Creatine deficiency Guanidinoacetate methyltransferase deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Creatine deficiency Creatine transporter deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Creatine deficiency X-linked creatine transporter deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cerebral creatine deficiency syndrome Guanidinoacetate methyltransferase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral creatine deficiency syndrome Creatine transporter deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cerebral creatine deficiency syndrome X-linked creatine transporter deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.