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 71

14 diseases · 15 shared-gene connections
14 Diseases
100 Unique genes
0.043 Avg. similarity score
Congenital disorder of glycosylation Most-connected disease (13 links)
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Disease Searched: Congenital disorder of glycosylation, type IIz 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 13 13 100
Congenital disorder of glycosylation, type IIz 3 3 3
Congenital disorder of glycosylation type 1a 2 2 1
Epileptic encephalopathy, early infantile, 22 (eiee22) 2 2 1
Combined low ldl and fibrinogen 1 1 1
Congenital disorder of glycosylation type 1E 1 1 1
Congenital disorder of glycosylation type iii 1 1 1
Congenital disorder of glycosylation type iy 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 Iw, autosomal dominant 1 1 1
Disorder of golgi homeostasis 1 1 1
Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LOC100130283 3 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation type 1a, Congenital disorder of glycosylation, type IIz
SLC35A2 3 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation, type IIz, Epileptic encephalopathy, early infantile, 22 (eiee22)
B4GALT1 2 / 14 Combined low ldl and fibrinogen, Congenital disorder of glycosylation
CAMLG 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation, type IIz
COG2 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation, type IIq
COG5 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation type iii
DPM1 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation type 1E
FCSK 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation with defective fucosylation 2
FUT8 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation with defective fucosylation 1
PIGF 2 / 14 Congenital disorder of glycosylation, Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome
SSR4 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation type iy
STT3A 2 / 14 Congenital disorder of glycosylation, Congenital disorder of glycosylation, type Iw, autosomal dominant
VMA22 2 / 14 Congenital disorder of glycosylation, Disorder of golgi homeostasis
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 65.5× 8.89e-50 1.14e-45 ✓ sig.
Various types of N-glycan biosynthesis
ALG11, ALG12, ALG1, ALG2, ALG3, ALG9, B4GALT1, ALG13, ALG14, DDOST, MAGT1, MAN2A2
 KEGG 19 / 43 53.1× 3.45e-29 1.00e-25 ✓ 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 / 11 120× 7.57e-24 1.06e-20 ✓ sig.
Metabolic pathways
A4GALT, ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B4GALT1, ALG10
 KEGG 46 / 1,563 3.5× 5.86e-16 2.14e-13 ✓ sig.
Intra-Golgi traffic
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3, MAN2A2, STX5
 Reactome 10 / 44 27.3× 1.99e-12 3.52e-10 ✓ sig.
Retrograde transport at the Trans-Golgi-Network
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 Reactome 8 / 46 20.9× 3.50e-9 2.89e-7 ✓ sig.
Asparagine N-linked glycosylation
DDOST, MAGT1, TUSC3, STT3A, RPN2
 Reactome 5 / 11 54.6× 1.61e-8 1.13e-6 ✓ sig.
Protein processing in endoplasmic reticulum
DDOST, MAGT1, SSR3, SSR4, TUSC3, STT3A, STT3B, EDEM3, MOGS, RPN2, UGGT1, MAN1B1
 KEGG 12 / 171 8.4× 1.67e-8 1.17e-6 ✓ sig.
Synthesis of Dolichyl-phosphate
SRD5A3, NUS1, DHDDS, DOLK
 Reactome 4 / 6 80.1× 6.70e-8 3.94e-6 ✓ sig.
COPI-mediated anterograde transport
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3, STX5
 Reactome 9 / 101 10.7× 1.48e-7 7.89e-6 ✓ sig.
Synthesis of glycosylphosphatidylinositol (GPI)
DPM2, PIGF, PIGM, PIGC, PIGW
 Reactome 5 / 17 35.3× 2.07e-7 1.06e-5 ✓ sig.
Biosynthesis of nucleotide sugars
GFUS, PGM1, PMM2, MPI, FCSK, PGM3
 KEGG 6 / 37 19.5× 5.40e-7 2.44e-5 ✓ sig.
Synthesis of dolichyl-phosphate mannose
DPM2, DPM1, DPM3
 Reactome 3 / 3 120× 5.60e-7 2.51e-5 ✓ sig.
Defective DPM1 causes DPM1-CDG (CDG-1e)
DPM2, DPM1, DPM3
 Reactome 3 / 3 120× 5.60e-7 2.51e-5 ✓ sig.
Defective DPM3 causes DPM3-CDG (CDG-1o)
DPM2, DPM1, DPM3
 Reactome 3 / 3 120× 5.60e-7 2.51e-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 28 / 62 84.4× 1.19e-48 2.16e-44 ✓ sig.
protein glycosylation
ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B4GALT1, COG7, ALG10, COG3
 GO:0006486 34 / 181 35.1× 4.44e-44 6.26e-40 ✓ sig.
dolichol-linked oligosaccharide biosynthetic process
ALG11, ALG12, ALG1, ALG2, ALG3, ALG6, ALG8, ALG9, ALG10, ALG13, ALG14, DPM2
 GO:0006488 17 / 19 167× 9.78e-38 1.01e-33 ✓ sig.
retrograde transport, vesicle recycling within Golgi
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0000301 8 / 9 166× 4.53e-18 5.45e-15 ✓ sig.
protein N-linked glycosylation via asparagine
ALG8, DDOST, MAGT1, TUSC3, DPM1, STT3A, STT3B, MGAT2, FUT8, UGGT1
 GO:0018279 10 / 24 77.9× 2.24e-17 2.45e-14 ✓ sig.
glycosylation
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0070085 8 / 20 74.7× 6.04e-14 3.64e-11 ✓ sig.
dolichyl monophosphate biosynthetic process
SRD5A3, DHRSX, NUS1, DHDDS, DOLK
 GO:0043048 5 / 5 187× 3.97e-12 1.66e-9 ✓ sig.
dolichol phosphate mannose biosynthetic process
DPM2, DPM1, DOLK, DPM3
 GO:0180047 4 / 4 187× 7.72e-10 1.85e-7 ✓ sig.
dolichyl diphosphate biosynthetic process
SRD5A3, NUS1, DHDDS, DOLK
 GO:0006489 4 / 5 149× 3.84e-9 7.60e-7 ✓ sig.
GPI anchor biosynthetic process
DPM2, DPM1, PIGF, PIGM, PIGC, PIGW
 GO:0006506 6 / 31 36.2× 1.33e-8 2.27e-6 ✓ sig.
intra-Golgi vesicle-mediated transport
COG1, COG2, COG5, COG6, COG8, COG3
 GO:0006891 6 / 32 35.0× 1.63e-8 2.70e-6 ✓ sig.
carbohydrate metabolic process
B4GALT1, MAN2A2, PGM1, MPI, MAN2B2, EDEM3, MOGS, SLC35A1, MAN1B1, PGM3
 GO:0005975 10 / 175 10.7× 3.36e-8 5.07e-6 ✓ sig.
Golgi organization
COG1, COG2, COG4, COG5, COG6, COG7, COG8, COG3
 GO:0007030 8 / 128 11.7× 4.27e-7 4.26e-5 ✓ sig.
proteoglycan biosynthetic process
B3GALT6, FAM20B, XYLT1, CSGALNACT1
 GO:0030166 4 / 21 35.6× 4.31e-6 2.81e-4 ✓ sig.
mannose metabolic process
MAN2A2, PMM2, MAN2B2
 GO:0006013 3 / 8 70.1× 8.17e-6 4.66e-4 ✓ 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 IIz 0.030 3 2.61e-7 1.72e-6 ✓ sig.
Congenital disorder of glycosylation type 1a Congenital disorder of glycosylation, type IIz 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital disorder of glycosylation, type IIz Epileptic encephalopathy, early infantile, 22 (eiee22) 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Combined low ldl and fibrinogen Congenital disorder of glycosylation 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation type 1a 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation type 1E 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation type iii 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation type iy 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation with defective fucosylation 1 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation with defective fucosylation 2 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation, type IIq 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Congenital disorder of glycosylation, type Iw, autosomal dominant 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Disorder of golgi homeostasis 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Epileptic encephalopathy, early infantile, 22 (eiee22) 0.010 1 6.46e-3 7.56e-3 ✓ sig.
Congenital disorder of glycosylation Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome 0.010 1 6.46e-3 7.56e-3 ✓ sig.