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 460

6 diseases · 12 shared-gene connections
6 Diseases
4 Unique genes
0.325 Avg. similarity score
Gm2 gangliosidosis 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 ⇵
Gm2 gangliosidosis 5 5 3
Tay-sachs disease 5 5 3
Beta-hexosaminidase a deficiency 4 4 1
Gm2-gangliosidosis, several forms, tay-sachs disease 4 4 1
Hex a pseudodeficiency 4 4 1
Hexosaminidase activator deficiency 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
HEXA 5 / 6 Beta-hexosaminidase a deficiency, Gm2 gangliosidosis, Gm2-gangliosidosis, several forms, tay-sachs disease, Hex a pseudodeficiency and 1 more
GM2A 3 / 6 Gm2 gangliosidosis, Hexosaminidase activator deficiency, Tay-sachs disease
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 ⇵
Glycosphingolipid metabolism
HEXA, GM2A, HEXB
 Reactome 3 / 46 196× 2.10e-7 1.07e-5 ✓ sig.
Sphingolipid metabolism
HEXA, GM2A, HEXB
 KEGG 3 / 54 167× 3.43e-7 1.64e-5 ✓ sig.
Lysosome
HEXA, GM2A, HEXB
 KEGG 3 / 133 67.7× 5.27e-6 1.71e-4 ✓ sig.
Hyaluronan uptake and degradation
HEXA, HEXB
 Reactome 2 / 12 500× 5.49e-6 1.77e-4 ✓ sig.
Keratan sulfate degradation
HEXA, HEXB
 Reactome 2 / 13 462× 6.48e-6 2.04e-4 ✓ sig.
CS/DS degradation
HEXA, HEXB
 Reactome 2 / 14 429× 7.56e-6 2.32e-4 ✓ sig.
Glycosphingolipid biosynthesis - ganglio series
HEXA, HEXB
 KEGG 2 / 15 400× 8.72e-6 2.60e-4 ✓ sig.
Glycosphingolipid biosynthesis - globo and isoglobo series
HEXA, HEXB
 KEGG 2 / 16 375× 9.97e-6 2.91e-4 ✓ sig.
Other glycan degradation
HEXA, HEXB
 KEGG 2 / 18 334× 1.27e-5 3.55e-4 ✓ sig.
Glycosaminoglycan degradation
HEXA, HEXB
 KEGG 2 / 19 316× 1.42e-5 3.90e-4 ✓ sig.
Amino sugar and nucleotide sugar metabolism
HEXA, HEXB
 KEGG 2 / 38 158× 5.83e-5 1.23e-3 ✓ sig.
Various types of N-glycan biosynthesis
HEXA, HEXB
 KEGG 2 / 43 140× 7.48e-5 1.50e-3 ✓ sig.
Defective HEXA causes GM2G1
HEXA
 Reactome 1 / 1 3,003× 3.33e-4 4.88e-3 ✓ sig.
Defective HEXB causes GM2G2
HEXB
 Reactome 1 / 1 3,003× 3.33e-4 4.88e-3 ✓ sig.
Neutrophil degranulation
GM2A, HEXB
 Reactome 2 / 480 12.5× 9.06e-3 5.36e-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 ⇵
ganglioside catabolic process
HEXA, GM2A, HEXB
 GO:0006689 3 / 8 1,752× 2.06e-10 5.84e-8 ✓ sig.
lipid storage
HEXA, GM2A, HEXB
 GO:0019915 3 / 32 438× 1.82e-8 2.97e-6 ✓ sig.
neuromuscular process controlling balance
HEXA, GM2A, HEXB
 GO:0050885 3 / 53 264× 8.60e-8 1.11e-5 ✓ sig.
dermatan sulfate proteoglycan catabolic process
HEXA, HEXB
 GO:0030209 2 / 4 2,336× 2.06e-7 2.32e-5 ✓ sig.
oligosaccharide catabolic process
GM2A, HEXB
 GO:0009313 2 / 12 779× 2.27e-6 1.68e-4 ✓ sig.
glycosaminoglycan metabolic process
HEXA, HEXB
 GO:0030203 2 / 12 779× 2.27e-6 1.68e-4 ✓ sig.
hyaluronan catabolic process
HEXA, HEXB
 GO:0030214 2 / 16 584× 4.12e-6 2.71e-4 ✓ sig.
sexual reproduction
HEXA, HEXB
 GO:0019953 2 / 17 550× 4.67e-6 3.01e-4 ✓ sig.
carbohydrate derivative metabolic process
HEXA, HEXB
 GO:1901135 2 / 18 519× 5.25e-6 3.29e-4 ✓ sig.
N-glycan processing
HEXA, HEXB
 GO:0006491 2 / 19 492× 5.87e-6 3.60e-4 ✓ sig.
lysosome organization
HEXA, HEXB
 GO:0007040 2 / 65 144× 7.12e-5 2.40e-3 ✓ sig.
myelination
HEXA, HEXB
 GO:0042552 2 / 73 128× 8.99e-5 2.86e-3 ✓ sig.
locomotory behavior
HEXA, HEXB
 GO:0007626 2 / 99 94.4× 1.66e-4 4.43e-3 ✓ sig.
positive regulation of termination of DNA-templated transcription
SETX
 GO:0060566 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
male courtship behavior
HEXB
 GO:0008049 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Gm2 gangliosidosis Tay-sachs disease 0.400 2 7.50e-8 5.34e-7 ✓ sig.
Beta-hexosaminidase a deficiency Hex a pseudodeficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Beta-hexosaminidase a deficiency Gm2-gangliosidosis, several forms, tay-sachs disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Gm2-gangliosidosis, several forms, tay-sachs disease Hex a pseudodeficiency 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Beta-hexosaminidase a deficiency Gm2 gangliosidosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Beta-hexosaminidase a deficiency Tay-sachs disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gm2 gangliosidosis Hex a pseudodeficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gm2 gangliosidosis Gm2-gangliosidosis, several forms, tay-sachs disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gm2 gangliosidosis Hexosaminidase activator deficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gm2-gangliosidosis, several forms, tay-sachs disease Tay-sachs disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hex a pseudodeficiency Tay-sachs disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Hexosaminidase activator deficiency Tay-sachs disease 0.250 1 1.94e-4 4.41e-4 ✓ sig.