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 222

8 diseases · 16 shared-gene connections
8 Diseases
5 Unique genes
0.359 Avg. similarity score
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome 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 ⇵
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome 5 5 3
Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome 5 5 1
Kenny caffey syndrome 5 5 1
Kenny-caffey syndrome 5 5 3
Sanjad-sakati syndrome 5 5 1
encephalopathy, progressive, with amyotrophy and optic atrophy 5 5 1
Seborrhea-like dermatitis with psoriasiform elements 1 1 2
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBCE 6 / 8 Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome, encephalopathy, progressive, with amyotrophy and optic atrophy, Kenny caffey syndrome and 2 more
B3GALNT2 2 / 8 Kenny-caffey syndrome, muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11
TBCD 2 / 8 Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, Seborrhea-like dermatitis with psoriasiform elements
ZNF750 2 / 8 Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, Seborrhea-like dermatitis with psoriasiform elements
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 ⇵
O-linked glycosylation
B3GALNT2
 Reactome 1 / 10 240× 4.16e-3 3.87e-2 ✓ sig.
Mannose type O-glycan biosynthesis
B3GALNT2
 KEGG 1 / 23 104× 9.54e-3 6.67e-2
Generic Transcription Pathway
ZNF750
 Reactome 1 / 346 6.9× 1.36e-1 2.93e-1
Metabolic pathways
B3GALNT2
 KEGG 1 / 1,563 1.5× 5.02e-1 6.44e-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 ⇵
post-chaperonin tubulin folding pathway
TBCE, TBCD
 GO:0007023 2 / 7 1,068× 1.20e-6 9.61e-5 ✓ sig.
tubulin complex assembly
TBCE, TBCD
 GO:0007021 2 / 10 747× 2.58e-6 1.76e-4 ✓ sig.
muscle atrophy
TBCE
 GO:0014889 1 / 2 1,869× 5.35e-4 9.98e-3 ✓ sig.
microtubule cytoskeleton organization
TBCE, TBCD
 GO:0000226 2 / 149 50.2× 6.22e-4 1.11e-2 ✓ sig.
peripheral nervous system neuron axonogenesis
TBCE
 GO:0048936 1 / 4 934× 1.07e-3 1.57e-2 ✓ sig.
protein folding
TBCE, TBCD
 GO:0006457 2 / 203 36.8× 1.15e-3 1.65e-2 ✓ sig.
membrane biogenesis
ZNF750
 GO:0044091 1 / 5 747× 1.34e-3 1.79e-2 ✓ sig.
positive regulation of ceramide biosynthetic process
ZNF750
 GO:2000304 1 / 7 534× 1.87e-3 2.19e-2 ✓ sig.
protein-DNA covalent cross-linking repair
FAM111A
 GO:0106300 1 / 9 415× 2.41e-3 2.50e-2 ✓ sig.
adherens junction assembly
TBCD
 GO:0034333 1 / 13 287× 3.47e-3 3.06e-2 ✓ sig.
negative regulation of microtubule polymerization
TBCD
 GO:0031115 1 / 13 287× 3.47e-3 3.06e-2 ✓ sig.
cell morphogenesis involved in neuron differentiation
TBCD
 GO:0048667 1 / 14 267× 3.74e-3 3.18e-2 ✓ sig.
negative regulation of cell-substrate adhesion
TBCD
 GO:0010812 1 / 18 208× 4.81e-3 3.58e-2 ✓ sig.
protein autoprocessing
FAM111A
 GO:0016540 1 / 25 149× 6.67e-3 4.26e-2 ✓ sig.
developmental growth
TBCE
 GO:0048589 1 / 30 125× 8.00e-3 4.60e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome Seborrhea-like dermatitis with psoriasiform elements 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome Kenny caffey syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome Sanjad-sakati syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome encephalopathy, progressive, with amyotrophy and optic atrophy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
encephalopathy, progressive, with amyotrophy and optic atrophy Kenny caffey syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
encephalopathy, progressive, with amyotrophy and optic atrophy Sanjad-sakati syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Kenny caffey syndrome Sanjad-sakati syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome Kenny caffey syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome Sanjad-sakati syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome encephalopathy, progressive, with amyotrophy and optic atrophy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome Kenny-caffey syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
encephalopathy, progressive, with amyotrophy and optic atrophy Kenny-caffey syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Kenny caffey syndrome Kenny-caffey syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Kenny-caffey syndrome Sanjad-sakati syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Kenny-caffey syndrome muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 0.250 1 1.95e-4 5.28e-4 ✓ sig.