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 5
39
Diseases
147
Unique genes
0.062
Avg. similarity score
Congenital disorder of glycosylation
Most-connected disease (25 links)
Disease
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Congenital disorder of glycosylation
Congenital myasthenic syndrome
Myasthenic syndrome
Postsynaptic congenital myasthenic syndrome
Presynaptic congenital myasthenic syndrome
Fetal akinesia deformation sequence
congenital myasthenic syndrome 8
ALG2-congenital disorder of glycosylation
Intellectual developmental disorder seizures behavioral
congenital myasthenic syndrome 10
congenital myasthenic syndrome 6
congenital myasthenic syndrome 7
congenital myasthenic syndrome 9
neuronopathy, distal hereditary motor, type 7A
Ataxia, spastic, autosomal dominant
congenital myasthenic syndrome 12
myasthenic syndrome, congenital, 1b, fast-channel
ALG1-congenital disorder of glycosylation
ALG12-congenital disorder of glycosylation
ALG3-congenital disorder of glycosylation
Alstrom syndrome
COG1-congenital disorder of glycosylation
COG5-congenital disorder of glycosylation
COG7-congenital disorder of glycosylation
COG8-congenital disorder of glycosylation
DK1-congenital disorder of glycosylation
DPM3-congenital disorder of glycosylation
MAN2B2 deficiency
MGAT2-congenital disorder of glycosylation
MOGS-congenital disorder of glycosylation
MPDU1-congenital disorder of glycosylation
RFT1-congenital disorder of glycosylation
SLC35A1-congenital disorder of glycosylation
Sandestig-stefanova syndrome
congenital disorder of glycosylation type 1E
congenital disorder of glycosylation with defective fucosylation 1
congenital disorder of glycosylation with defective fucosylation 2
congenital disorder of glycosylation, type IIq
congenital disorder of glycosylation, type IIz
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| AGRN | 5 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 8, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome and 1 more |
| DOK7 | 5 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 10, Fetal akinesia deformation sequence, Myasthenic syndrome and 1 more |
| MUSK | 5 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 9, Fetal akinesia deformation sequence, Myasthenic syndrome and 1 more |
| ALG14 | 4 / 39 | Congenital disorder of glycosylation, Congenital myasthenic syndrome, Intellectual developmental disorder seizures behavioral, Myasthenic syndrome |
| ALG2 | 4 / 39 | ALG2-congenital disorder of glycosylation, Congenital disorder of glycosylation, Congenital myasthenic syndrome, Myasthenic syndrome |
| CHAT | 4 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 6, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| CHRNA1 | 4 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, myasthenic syndrome, congenital, 1b, fast-channel, Postsynaptic congenital myasthenic syndrome |
| COL13A1 | 4 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| RAPSN | 4 / 39 | Congenital myasthenic syndrome, Fetal akinesia deformation sequence, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| SLC18A3 | 4 / 39 | Congenital myasthenic syndrome, Fetal akinesia deformation sequence, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| SLC5A7 | 4 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, neuronopathy, distal hereditary motor, type 7A, Presynaptic congenital myasthenic syndrome |
| SYT2 | 4 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 7, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| CHRNB1 | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| CHRND | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| CHRNE | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| DPAGT1 | 3 / 39 | Congenital disorder of glycosylation, Congenital myasthenic syndrome, Myasthenic syndrome |
| GFPT1 | 3 / 39 | Congenital myasthenic syndrome, congenital myasthenic syndrome 12, Myasthenic syndrome |
| LRP4 | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| MYO9A | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| SCN4A | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Postsynaptic congenital myasthenic syndrome |
| SLC25A1 | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| SNAP25 | 3 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| VAMP1 | 3 / 39 | Ataxia, spastic, autosomal dominant, Myasthenic syndrome, Presynaptic congenital myasthenic syndrome |
| ALG1 | 2 / 39 | ALG1-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| ALG12 | 2 / 39 | ALG12-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| ALG3 | 2 / 39 | ALG3-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| ALMS1 | 2 / 39 | Alstrom syndrome, Fetal akinesia deformation sequence |
| CAMLG | 2 / 39 | Congenital disorder of glycosylation, congenital disorder of glycosylation, type IIz |
| CHD8 | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| COG1 | 2 / 39 | COG1-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| COG2 | 2 / 39 | Congenital disorder of glycosylation, congenital disorder of glycosylation, type IIq |
| COG5 | 2 / 39 | COG5-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| COG7 | 2 / 39 | COG7-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| COG8 | 2 / 39 | COG8-congenital disorder of glycosylation, Congenital disorder of glycosylation |
| COLQ | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| DOLK | 2 / 39 | Congenital disorder of glycosylation, DK1-congenital disorder of glycosylation |
| DPM1 | 2 / 39 | Congenital disorder of glycosylation, congenital disorder of glycosylation type 1E |
| DPM3 | 2 / 39 | Congenital disorder of glycosylation, DPM3-congenital disorder of glycosylation |
| FCSK | 2 / 39 | Congenital disorder of glycosylation, congenital disorder of glycosylation with defective fucosylation 2 |
| FUT8 | 2 / 39 | Congenital disorder of glycosylation, congenital disorder of glycosylation with defective fucosylation 1 |
| GMPPB | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| MAN2B2 | 2 / 39 | Congenital disorder of glycosylation, MAN2B2 deficiency |
| MGAT2 | 2 / 39 | Congenital disorder of glycosylation, MGAT2-congenital disorder of glycosylation |
| MOGS | 2 / 39 | Congenital disorder of glycosylation, MOGS-congenital disorder of glycosylation |
| MPDU1 | 2 / 39 | Congenital disorder of glycosylation, MPDU1-congenital disorder of glycosylation |
| NUP188 | 2 / 39 | Congenital disorder of glycosylation, Sandestig-stefanova syndrome |
| PLEC | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| PREPL | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| RFT1 | 2 / 39 | Congenital disorder of glycosylation, RFT1-congenital disorder of glycosylation |
| RPH3A | 2 / 39 | Congenital myasthenic syndrome, Myasthenic syndrome |
| SLC35A1 | 2 / 39 | Congenital disorder of glycosylation, SLC35A1-congenital disorder of glycosylation |
| TAPBPL | 2 / 39 | Ataxia, spastic, autosomal dominant, Myasthenic syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| N-Glycan biosynthesis | KEGG | 30 / 55 | 44.6× | 4.51e-44 | 3.83e-40 ✓ sig. |
| Various types of N-glycan biosynthesis | KEGG | 19 / 43 | 36.1× | 8.77e-26 | 1.76e-22 ✓ sig. |
| Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | Reactome | 11 / 11 | 81.7× | 6.32e-22 | 7.13e-19 ✓ sig. |
| Intra-Golgi traffic | Reactome | 10 / 44 | 18.6× | 9.64e-11 | 1.39e-8 ✓ sig. |
| Metabolic pathways | KEGG | 48 / 1,563 | 2.5× | 4.92e-10 | 6.02e-8 ✓ sig. |
| Retrograde transport at the Trans-Golgi-Network | Reactome | 8 / 46 | 14.2× | 7.33e-8 | 4.98e-6 ✓ sig. |
| Asparagine N-linked glycosylation | Reactome | 5 / 11 | 37.1× | 1.12e-7 | 7.21e-6 ✓ sig. |
| Biosynthesis of nucleotide sugars | KEGG | 7 / 37 | 15.5× | 2.70e-7 | 1.56e-5 ✓ sig. |
| Synthesis of Dolichyl-phosphate | Reactome | 4 / 6 | 54.5× | 3.17e-7 | 1.80e-5 ✓ sig. |
| COPI-mediated anterograde transport | Reactome | 10 / 101 | 8.1× | 4.12e-7 | 2.26e-5 ✓ sig. |
| Protein processing in endoplasmic reticulum | KEGG | 12 / 171 | 5.7× | 1.20e-6 | 5.71e-5 ✓ sig. |
| Synthesis of glycosylphosphatidylinositol (GPI) | Reactome | 5 / 17 | 24.0× | 1.41e-6 | 6.58e-5 ✓ sig. |
| Synthesis of dolichyl-phosphate mannose | Reactome | 3 / 3 | 81.7× | 1.80e-6 | 8.04e-5 ✓ sig. |
| Defective DPM1 causes DPM1-CDG (CDG-1e) | Reactome | 3 / 3 | 81.7× | 1.80e-6 | 8.04e-5 ✓ sig. |
| Defective DPM3 causes DPM3-CDG (CDG-1o) | Reactome | 3 / 3 | 81.7× | 1.80e-6 | 8.04e-5 ✓ sig. |
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 N-linked glycosylation | GO:0006487 | 28 / 62 | 57.4× | 2.23e-43 | 3.26e-39 ✓ sig. |
| protein glycosylation | GO:0006486 | 35 / 181 | 24.6× | 3.59e-39 | 3.49e-35 ✓ sig. |
| dolichol-linked oligosaccharide biosynthetic process | GO:0006488 | 17 / 19 | 114× | 1.10e-34 | 8.18e-31 ✓ sig. |
| retrograde transport, vesicle recycling within Golgi | GO:0000301 | 8 / 9 | 113× | 1.08e-16 | 1.02e-13 ✓ sig. |
| protein N-linked glycosylation via asparagine | GO:0018279 | 10 / 24 | 53.0× | 1.19e-15 | 9.05e-13 ✓ sig. |
| glycosylation | GO:0070085 | 8 / 20 | 50.8× | 1.41e-12 | 6.28e-10 ✓ sig. |
| dolichyl monophosphate biosynthetic process | GO:0043048 | 5 / 5 | 127× | 2.81e-11 | 9.19e-9 ✓ sig. |
| synaptic transmission, cholinergic | GO:0007271 | 7 / 25 | 35.6× | 6.89e-10 | 1.61e-7 ✓ sig. |
| dolichol phosphate mannose biosynthetic process | GO:0180047 | 4 / 4 | 127× | 3.68e-9 | 7.10e-7 ✓ sig. |
| dolichyl diphosphate biosynthetic process | GO:0006489 | 4 / 5 | 102× | 1.83e-8 | 2.88e-6 ✓ sig. |
| GPI anchor biosynthetic process | GO:0006506 | 6 / 31 | 24.6× | 1.34e-7 | 1.54e-5 ✓ sig. |
| intra-Golgi vesicle-mediated transport | GO:0006891 | 6 / 32 | 23.8× | 1.64e-7 | 1.83e-5 ✓ sig. |
| cellular response to increased oxygen levels | GO:0036295 | 4 / 8 | 63.6× | 2.51e-7 | 2.63e-5 ✓ sig. |
| neuromuscular junction development | GO:0007528 | 6 / 35 | 21.8× | 2.88e-7 | 2.94e-5 ✓ sig. |
| skeletal muscle acetylcholine-gated channel clustering | GO:0071340 | 4 / 9 | 56.5× | 4.49e-7 | 4.27e-5 ✓ sig. |