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 14

22 diseases · 21 shared-gene connections
22 Diseases
99 Unique genes
0.010 Avg. similarity score
Congenital disorder of glycosylation Most-connected disease (21 links)
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Disease Searched: MOGS-congenital disorder of glycosylation 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 ⇵
Congenital disorder of glycosylation 21 21 99
ALG1-congenital disorder of glycosylation 1 1 1
ALG12-congenital disorder of glycosylation 1 1 1
ALG3-congenital disorder of glycosylation 1 1 1
COG1-congenital disorder of glycosylation 1 1 1
COG5-congenital disorder of glycosylation 1 1 1
COG7-congenital disorder of glycosylation 1 1 1
COG8-congenital disorder of glycosylation 1 1 1
DK1-congenital disorder of glycosylation 1 1 1
DPM3-congenital disorder of glycosylation 1 1 1
MAN2B2 deficiency 1 1 1
MGAT2-congenital disorder of glycosylation 1 1 1
MOGS-congenital disorder of glycosylation 1 1 1
MPDU1-congenital disorder of glycosylation 1 1 1
RFT1-congenital disorder of glycosylation 1 1 1
SLC35A1-congenital disorder of glycosylation 1 1 1
Sandestig-stefanova syndrome 1 1 1
congenital disorder of glycosylation type 1E 1 1 1
congenital disorder of glycosylation with defective fucosylation 1 1 1 1
congenital disorder of glycosylation with defective fucosylation 2 1 1 1
congenital disorder of glycosylation, type IIq 1 1 1
congenital disorder of glycosylation, type IIz 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ALG1 2 / 22 ALG1-congenital disorder of glycosylation, Congenital disorder of glycosylation
ALG12 2 / 22 ALG12-congenital disorder of glycosylation, Congenital disorder of glycosylation
ALG3 2 / 22 ALG3-congenital disorder of glycosylation, Congenital disorder of glycosylation
CAMLG 2 / 22 Congenital disorder of glycosylation, congenital disorder of glycosylation, type IIz
COG1 2 / 22 COG1-congenital disorder of glycosylation, Congenital disorder of glycosylation
COG2 2 / 22 Congenital disorder of glycosylation, congenital disorder of glycosylation, type IIq
COG5 2 / 22 COG5-congenital disorder of glycosylation, Congenital disorder of glycosylation
COG7 2 / 22 COG7-congenital disorder of glycosylation, Congenital disorder of glycosylation
COG8 2 / 22 COG8-congenital disorder of glycosylation, Congenital disorder of glycosylation
DOLK 2 / 22 Congenital disorder of glycosylation, DK1-congenital disorder of glycosylation
DPM1 2 / 22 Congenital disorder of glycosylation, congenital disorder of glycosylation type 1E
DPM3 2 / 22 Congenital disorder of glycosylation, DPM3-congenital disorder of glycosylation
FCSK 2 / 22 Congenital disorder of glycosylation, congenital disorder of glycosylation with defective fucosylation 2
FUT8 2 / 22 Congenital disorder of glycosylation, congenital disorder of glycosylation with defective fucosylation 1
MAN2B2 2 / 22 Congenital disorder of glycosylation, MAN2B2 deficiency
MGAT2 2 / 22 Congenital disorder of glycosylation, MGAT2-congenital disorder of glycosylation
MOGS 2 / 22 Congenital disorder of glycosylation, MOGS-congenital disorder of glycosylation
MPDU1 2 / 22 Congenital disorder of glycosylation, MPDU1-congenital disorder of glycosylation
NUP188 2 / 22 Congenital disorder of glycosylation, Sandestig-stefanova syndrome
RFT1 2 / 22 Congenital disorder of glycosylation, RFT1-congenital disorder of glycosylation
SLC35A1 2 / 22 Congenital disorder of glycosylation, SLC35A1-congenital disorder of glycosylation
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
ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B4GALT1, ALG10, ALG13, ALG14
 KEGG 30 / 55 66.2× 6.23e-50 8.65e-46 ✓ sig.
Various types of N-glycan biosynthesis
ALG11, ALG12, ALG1, ALG2, ALG3, ALG9, B4GALT1, ALG13, ALG14, DDOST, MAGT1, MAN2A2
 KEGG 19 / 43 53.6× 2.80e-29 6.91e-26 ✓ sig.
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, ALG13, ALG14, MPDU1, DPAGT1
 Reactome 11 / 11 121× 6.74e-24 9.12e-21 ✓ sig.
Metabolic pathways
A4GALT, ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B4GALT1, ALG10
 KEGG 44 / 1,563 3.4× 1.20e-14 3.33e-12 ✓ sig.
Intra-Golgi traffic
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3, MAN2A2, STX5
 Reactome 10 / 44 27.6× 1.79e-12 3.42e-10 ✓ sig.
Retrograde transport at the Trans-Golgi-Network
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 Reactome 8 / 46 21.1× 3.23e-9 3.05e-7 ✓ sig.
Protein processing in endoplasmic reticulum
DDOST, MAGT1, SSR3, SSR4, TUSC3, STT3A, STT3B, EDEM3, MOGS, RPN2, UGGT1, MAN1B1
 KEGG 12 / 171 8.5× 1.49e-8 1.17e-6 ✓ sig.
Asparagine N-linked glycosylation
DDOST, MAGT1, TUSC3, STT3A, RPN2
 Reactome 5 / 11 55.1× 1.53e-8 1.19e-6 ✓ sig.
Synthesis of Dolichyl-phosphate
SRD5A3, NUS1, DHDDS, DOLK
 Reactome 4 / 6 80.9× 6.43e-8 4.31e-6 ✓ sig.
COPI-mediated anterograde transport
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3, STX5
 Reactome 9 / 101 10.8× 1.36e-7 8.28e-6 ✓ sig.
Synthesis of glycosylphosphatidylinositol (GPI)
DPM2, PIGF, PIGM, PIGC, PIGW
 Reactome 5 / 17 35.7× 1.97e-7 1.13e-5 ✓ sig.
Synthesis of dolichyl-phosphate mannose
DPM2, DPM1, DPM3
 Reactome 3 / 3 121× 5.43e-7 2.75e-5 ✓ sig.
Defective DPM1 causes DPM1-CDG (CDG-1e)
DPM2, DPM1, DPM3
 Reactome 3 / 3 121× 5.43e-7 2.75e-5 ✓ sig.
Defective DPM3 causes DPM3-CDG (CDG-1o)
DPM2, DPM1, DPM3
 Reactome 3 / 3 121× 5.43e-7 2.75e-5 ✓ sig.
Defective DPM2 causes DPM2-CDG (CDG-1u)
DPM2, DPM1, DPM3
 Reactome 3 / 3 121× 5.43e-7 2.75e-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
ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B4GALT1, ALG10, ALG13, ALG14
 GO:0006487 27 / 62 82.2× 1.78e-46 2.85e-42 ✓ sig.
protein glycosylation
ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B4GALT1, COG7, ALG10, COG3
 GO:0006486 34 / 181 35.5× 2.95e-44 4.53e-40 ✓ sig.
dolichol-linked oligosaccharide biosynthetic process
ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, ALG10, ALG13, ALG14, DPM2
 GO:0006488 17 / 19 169× 8.12e-38 7.34e-34 ✓ sig.
retrograde transport, vesicle recycling within Golgi
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0000301 8 / 9 168× 4.17e-18 4.86e-15 ✓ sig.
protein N-linked glycosylation via asparagine
ALG8, DDOST, MAGT1, TUSC3, DPM1, STT3A, STT3B, MGAT2, FUT8, UGGT1
 GO:0018279 10 / 24 78.6× 2.01e-17 2.11e-14 ✓ sig.
glycosylation
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0070085 8 / 20 75.5× 5.56e-14 3.24e-11 ✓ sig.
dolichyl monophosphate biosynthetic process
SRD5A3, DHRSX, NUS1, DHDDS, DOLK
 GO:0043048 5 / 5 189× 3.77e-12 1.52e-9 ✓ sig.
dolichol phosphate mannose biosynthetic process
DPM2, DPM1, DOLK, DPM3
 GO:0180047 4 / 4 189× 7.41e-10 1.72e-7 ✓ sig.
dolichyl diphosphate biosynthetic process
SRD5A3, NUS1, DHDDS, DOLK
 GO:0006489 4 / 5 151× 3.69e-9 7.04e-7 ✓ sig.
GPI anchor biosynthetic process
DPM2, DPM1, PIGF, PIGM, PIGC, PIGW
 GO:0006506 6 / 31 36.5× 1.25e-8 2.06e-6 ✓ sig.
intra-Golgi vesicle-mediated transport
COG1, COG2, COG5, COG6, COG8, COG3
 GO:0006891 6 / 32 35.4× 1.54e-8 2.46e-6 ✓ sig.
cellular response to increased oxygen levels
CCDC115, ATP6V0A2, ATP6AP1, TMEM199
 GO:0036295 4 / 8 94.4× 5.10e-8 6.82e-6 ✓ sig.
lysosomal lumen acidification
CCDC115, ATP6AP1, ATP6AP2, TMEM199, VMA21
 GO:0007042 5 / 25 37.8× 1.84e-7 2.02e-5 ✓ sig.
carbohydrate metabolic process
B4GALT1, MAN2A2, PGM1, MPI, MAN2B2, EDEM3, MOGS, SLC35A1, MAN1B1
 GO:0005975 9 / 175 9.7× 3.79e-7 3.68e-5 ✓ sig.
Golgi organization
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0007030 8 / 128 11.8× 3.95e-7 3.82e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital disorder of glycosylation congenital disorder of glycosylation, type IIq 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation SLC35A1-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation Sandestig-stefanova syndrome 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation RFT1-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation MPDU1-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation MOGS-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation MGAT2-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation MAN2B2 deficiency 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation DPM3-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation DK1-congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation congenital disorder of glycosylation, type IIz 0.010 1 6.43e-3 7.68e-3 ✓ sig.
ALG1-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation congenital disorder of glycosylation with defective fucosylation 2 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation congenital disorder of glycosylation with defective fucosylation 1 0.010 1 6.43e-3 7.68e-3 ✓ sig.
Congenital disorder of glycosylation congenital disorder of glycosylation type 1E 0.010 1 6.43e-3 7.68e-3 ✓ sig.
COG8-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
COG7-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
COG5-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
COG1-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
ALG3-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.
ALG12-congenital disorder of glycosylation Congenital disorder of glycosylation 0.010 1 6.43e-3 7.68e-3 ✓ sig.