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 100

12 diseases · 39 shared-gene connections
12 Diseases
37 Unique genes
0.172 Avg. similarity score
Vitamin b deficiency Most-connected disease (11 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 ⇵
Vitamin b deficiency 11 11 12
Megaloblastic anemia 10 10 12
Vitamin b12 deficiency 10 10 11
Vitamin deficiency disorder 9 9 9
Deficiency anemia 7 7 24
Transcobalamin deficiency 6 6 2
Bombay phenotype 5 5 2
Vitamin b12-unresponsive methylmalonic acidemia 5 5 1
transcobalamin ii deficiency 5 5 1
methylmalonic aciduria, cblA type 4 4 1
Imerslund-grasbeck syndrome 3 3 3
methylmalonic acidemia due to transcobalamin receptor defect 3 3 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FUT2 7 / 12 Bombay phenotype, Deficiency anemia, Megaloblastic anemia, Vitamin b deficiency and 3 more
TCN2 7 / 12 Deficiency anemia, Megaloblastic anemia, Transcobalamin deficiency, transcobalamin ii deficiency and 3 more
CUBN 6 / 12 Deficiency anemia, Imerslund-grasbeck syndrome, Megaloblastic anemia, Vitamin b deficiency and 2 more
TCN1 6 / 12 Deficiency anemia, Megaloblastic anemia, Transcobalamin deficiency, Vitamin b deficiency and 2 more
MMAA 5 / 12 Deficiency anemia, Megaloblastic anemia, methylmalonic aciduria, cblA type, Vitamin b deficiency and 1 more
OOSP3 5 / 12 Deficiency anemia, Megaloblastic anemia, Vitamin b deficiency, Vitamin b12 deficiency and 1 more
CD320 4 / 12 Deficiency anemia, methylmalonic acidemia due to transcobalamin receptor defect, Vitamin b deficiency, Vitamin b12 deficiency
AMN 3 / 12 Imerslund-grasbeck syndrome, Megaloblastic anemia, Vitamin b deficiency
FUT6 3 / 12 Deficiency anemia, Vitamin b deficiency, Vitamin b12 deficiency
MMUT 3 / 12 Deficiency anemia, Vitamin b deficiency, Vitamin b12 deficiency
CDC42BPB 2 / 12 Imerslund-grasbeck syndrome, Megaloblastic anemia
FUT3 2 / 12 Deficiency anemia, Vitamin b12 deficiency
LRRC43 2 / 12 Deficiency anemia, Vitamin b12 deficiency
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 ⇵
Cobalamin (Cbl, vitamin B12) transport and metabolism
AMN, CUBN, TCN1, TCN2, CD320, MMAA, MMUT, ABCD4
 Reactome 8 / 21 124× 7.13e-16 2.81e-13 ✓ sig.
Cobalamin transport and metabolism
TCN1, TCN2, CD320, MMAA, MMUT, ABCD4
 KEGG 6 / 18 108× 1.01e-11 1.81e-9 ✓ sig.
Vitamin digestion and absorption
AMN, CUBN, SLC19A2, TCN2, SLC19A1, ABCD4
 KEGG 6 / 26 74.9× 1.23e-10 1.74e-8 ✓ sig.
Glycosphingolipid biosynthesis - lacto and neolacto series
FUT1, FUT2, FUT3, FUT6
 KEGG 4 / 28 46.4× 1.48e-6 6.85e-5 ✓ sig.
Vitamin D (calciferol) metabolism
CUBN, CYP2R1, GC
 Reactome 3 / 11 88.5× 4.37e-6 1.70e-4 ✓ sig.
Defective MMAA causes methylmalonic aciduria type cblA
MMAA, MMUT
 Reactome 2 / 2 325× 9.24e-6 3.14e-4 ✓ sig.
Defective MUT causes methylmalonic aciduria mut type
MMAA, MMUT
 Reactome 2 / 2 325× 9.24e-6 3.14e-4 ✓ sig.
Defective CD320 causes methylmalonic aciduria
TCN2, CD320
 Reactome 2 / 2 325× 9.24e-6 3.14e-4 ✓ sig.
Metabolism of folate and pterines
DHFR, MTHFR, SLC19A1
 Reactome 3 / 17 57.3× 1.78e-5 5.42e-4 ✓ sig.
Lewis blood group biosynthesis
FUT2, FUT3, FUT6
 Reactome 3 / 18 54.1× 2.13e-5 6.29e-4 ✓ sig.
ABO blood group biosynthesis
FUT1, FUT2
 Reactome 2 / 3 216× 2.77e-5 7.77e-4 ✓ sig.
Defective AMN causes hereditary megaloblastic anemia 1
AMN, CUBN
 Reactome 2 / 3 216× 2.77e-5 7.77e-4 ✓ sig.
Defective CUBN causes hereditary megaloblastic anemia 1
AMN, CUBN
 Reactome 2 / 3 216× 2.77e-5 7.77e-4 ✓ sig.
Propionyl-CoA catabolism
MMAA, MMUT
 Reactome 2 / 5 130× 9.18e-5 2.09e-3 ✓ sig.
HDL clearance
AMN, CUBN
 Reactome 2 / 5 130× 9.18e-5 2.09e-3 ✓ 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 ⇵
cobalamin transport
AMN, CUBN, TCN1, TCN2, CD320, ABCD4
 GO:0015889 6 / 9 337× 3.29e-15 2.38e-12 ✓ sig.
cobalamin metabolic process
AMN, CUBN, MMAA, ABCD4
 GO:0009235 4 / 9 224× 1.63e-9 3.46e-7 ✓ sig.
oligosaccharide biosynthetic process
FUT1, FUT2, FUT3, FUT6
 GO:0009312 4 / 26 77.7× 1.88e-7 2.06e-5 ✓ sig.
vitamin transport
SLC19A2, SLC19A1, GC
 GO:0051180 3 / 10 152× 8.49e-7 7.26e-5 ✓ sig.
L-fucose catabolic process
FUT1, FUT2, FUT6
 GO:0042355 3 / 10 152× 8.49e-7 7.26e-5 ✓ sig.
fucosylation
FUT1, FUT2, FUT3
 GO:0036065 3 / 12 126× 1.55e-6 1.18e-4 ✓ sig.
glycosphingolipid biosynthetic process
FUT1, FUT2, FUT6
 GO:0006688 3 / 25 60.6× 1.59e-5 7.54e-4 ✓ sig.
folic acid transport
SLC19A2, SLC19A1
 GO:0015884 2 / 8 126× 1.06e-4 3.16e-3 ✓ sig.
cobalt ion transport
TCN1, TCN2
 GO:0006824 2 / 8 126× 1.06e-4 3.16e-3 ✓ sig.
regulation of endothelial cell proliferation
FUT1, FUT2
 GO:0001936 2 / 9 112× 1.36e-4 3.80e-3 ✓ sig.
homocysteine metabolic process
MMUT, MTHFR
 GO:0050667 2 / 10 101× 1.70e-4 4.50e-3 ✓ sig.
tetrahydrofolate metabolic process
DHFR, MTHFR
 GO:0046653 2 / 11 91.8× 2.07e-4 5.18e-3 ✓ sig.
vitamin D metabolic process
CYP2R1, GC
 GO:0042359 2 / 12 84.2× 2.49e-4 5.90e-3 ✓ sig.
folic acid metabolic process
DHFR, SLC19A1
 GO:0046655 2 / 15 67.3× 3.94e-4 8.11e-3 ✓ sig.
protein glycosylation
FUT1, FUT2, FUT3, FUT6
 GO:0006486 4 / 181 11.2× 4.38e-4 8.72e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deficiency anemia Vitamin b12 deficiency 0.440 11 8.67e-33 3.07e-31 ✓ sig.
Vitamin b deficiency Vitamin b12 deficiency 0.600 9 9.04e-29 2.79e-27 ✓ sig.
Deficiency anemia Vitamin b deficiency 0.321 9 2.14e-24 5.32e-23 ✓ sig.
Megaloblastic anemia Vitamin b deficiency 0.389 7 1.54e-20 3.19e-19 ✓ sig.
Megaloblastic anemia Vitamin b12 deficiency 0.333 6 2.30e-17 4.04e-16 ✓ sig.
Deficiency anemia Megaloblastic anemia 0.194 6 6.68e-15 1.00e-13 ✓ sig.
Vitamin b12 deficiency Vitamin deficiency disorder 0.313 5 8.06e-15 1.20e-13 ✓ sig.
Vitamin b deficiency Vitamin deficiency disorder 0.294 5 1.38e-14 2.03e-13 ✓ sig.
Megaloblastic anemia Vitamin deficiency disorder 0.294 5 1.38e-14 2.03e-13 ✓ sig.
Deficiency anemia Vitamin deficiency disorder 0.172 5 7.40e-13 9.56e-12 ✓ sig.
Imerslund-grasbeck syndrome Megaloblastic anemia 0.231 3 3.62e-10 3.63e-9 ✓ sig.
Transcobalamin deficiency Vitamin deficiency disorder 0.200 2 3.04e-7 2.06e-6 ✓ sig.
Transcobalamin deficiency Vitamin b12 deficiency 0.167 2 4.64e-7 3.06e-6 ✓ sig.
Transcobalamin deficiency Vitamin b deficiency 0.154 2 5.57e-7 3.60e-6 ✓ sig.
Megaloblastic anemia Transcobalamin deficiency 0.154 2 5.57e-7 3.60e-6 ✓ sig.
Imerslund-grasbeck syndrome Vitamin b deficiency 0.143 2 1.67e-6 9.97e-6 ✓ sig.
Deficiency anemia Transcobalamin deficiency 0.080 2 2.33e-6 1.35e-5 ✓ sig.
Transcobalamin deficiency transcobalamin ii deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Bombay phenotype Vitamin b12-unresponsive methylmalonic acidemia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Vitamin b12-unresponsive methylmalonic acidemia Vitamin deficiency disorder 0.100 1 5.84e-4 1.14e-3 ✓ sig.
transcobalamin ii deficiency Vitamin deficiency disorder 0.100 1 5.84e-4 1.14e-3 ✓ sig.
methylmalonic aciduria, cblA type Vitamin b12 deficiency 0.083 1 7.14e-4 1.31e-3 ✓ sig.
transcobalamin ii deficiency Vitamin b12 deficiency 0.083 1 7.14e-4 1.31e-3 ✓ sig.
methylmalonic acidemia due to transcobalamin receptor defect Vitamin b12 deficiency 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Vitamin b12 deficiency Vitamin b12-unresponsive methylmalonic acidemia 0.083 1 7.14e-4 1.31e-3 ✓ sig.
transcobalamin ii deficiency Vitamin b deficiency 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Megaloblastic anemia transcobalamin ii deficiency 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Megaloblastic anemia Vitamin b12-unresponsive methylmalonic acidemia 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Vitamin b deficiency Vitamin b12-unresponsive methylmalonic acidemia 0.077 1 7.79e-4 1.39e-3 ✓ sig.
methylmalonic aciduria, cblA type Vitamin b deficiency 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Megaloblastic anemia methylmalonic aciduria, cblA type 0.077 1 7.79e-4 1.39e-3 ✓ sig.
methylmalonic acidemia due to transcobalamin receptor defect Vitamin b deficiency 0.077 1 7.79e-4 1.39e-3 ✓ sig.
Bombay phenotype Vitamin deficiency disorder 0.091 1 1.17e-3 1.88e-3 ✓ sig.
Bombay phenotype Vitamin b12 deficiency 0.077 1 1.43e-3 2.21e-3 ✓ sig.
Bombay phenotype Vitamin b deficiency 0.071 1 1.56e-3 2.36e-3 ✓ sig.
Bombay phenotype Megaloblastic anemia 0.071 1 1.56e-3 2.36e-3 ✓ sig.
Deficiency anemia methylmalonic aciduria, cblA type 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Deficiency anemia methylmalonic acidemia due to transcobalamin receptor defect 0.040 1 1.56e-3 2.36e-3 ✓ sig.
Imerslund-grasbeck syndrome Vitamin deficiency disorder 0.083 1 1.75e-3 2.59e-3 ✓ sig.