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 614

5 diseases · 8 shared-gene connections
5 Diseases
4 Unique genes
0.331 Avg. similarity score
Combined immunodeficiency, enteropathy spectrum Most-connected disease (4 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 ⇵
Combined immunodeficiency, enteropathy spectrum 4 4 3
Gastrointestinal defects and immunodeficiency syndrome 4 4 3
Intestinal atresia, inflammatory bowel disease and immunodeficiency 3 3 1
Multiple intestinal atresia 3 3 1
Combined factor v and factor viii deficiency 2 2 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
TTC7A 4 / 5 Combined immunodeficiency, enteropathy spectrum, Gastrointestinal defects and immunodeficiency syndrome, Intestinal atresia, inflammatory bowel disease and immunodeficiency, Multiple intestinal atresia
MCFD2 3 / 5 Combined factor v and factor viii deficiency, Combined immunodeficiency, enteropathy spectrum, Gastrointestinal defects and immunodeficiency syndrome
PI4KA 2 / 5 Combined immunodeficiency, enteropathy spectrum, Gastrointestinal defects and immunodeficiency 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 ⇵
Transport to the Golgi and subsequent modification
LMAN1, MCFD2
 Reactome 2 / 2 3,003× 8.32e-8 4.75e-6 ✓ sig.
Cargo concentration in the ER
LMAN1, MCFD2
 Reactome 2 / 33 182× 4.38e-5 9.84e-4 ✓ sig.
COPII-mediated vesicle transport
LMAN1, MCFD2
 Reactome 2 / 68 88.3× 1.88e-4 3.13e-3 ✓ sig.
Synthesis of PIPs at the ER membrane
PI4KA
 Reactome 1 / 5 601× 1.66e-3 1.66e-2 ✓ sig.
Synthesis of PIPs at the Golgi membrane
PI4KA
 Reactome 1 / 18 167× 5.98e-3 4.10e-2 ✓ sig.
Inositol phosphate metabolism
PI4KA
 KEGG 1 / 73 41.1× 2.41e-2 9.55e-2
Phosphatidylinositol signaling system
PI4KA
 KEGG 1 / 98 30.6× 3.22e-2 1.13e-1
Protein processing in endoplasmic reticulum
LMAN1
 KEGG 1 / 171 17.6× 5.58e-2 1.54e-1
Metabolic pathways
PI4KA
 KEGG 1 / 1,563 1.9× 4.28e-1 5.52e-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 ⇵
phosphatidylinositol phosphate biosynthetic process
PI4KA, TTC7A
 GO:0046854 2 / 43 217× 3.09e-5 1.28e-3 ✓ sig.
reorganization of cellular membranes to establish viral sites of replication
PI4KA
 GO:0140754 1 / 1 4,672× 2.14e-4 5.31e-3 ✓ sig.
positive regulation of organelle organization
LMAN1
 GO:0010638 1 / 4 1,168× 8.56e-4 1.33e-2 ✓ sig.
gene expression
LMAN1, MCFD2
 GO:0010467 2 / 269 34.7× 1.22e-3 1.63e-2 ✓ sig.
negative regulation of protein targeting to mitochondrion
LMAN1
 GO:1903215 1 / 6 779× 1.28e-3 1.67e-2 ✓ sig.
host-mediated perturbation of viral process
PI4KA
 GO:0044788 1 / 8 584× 1.71e-3 1.96e-2 ✓ sig.
vesicle-mediated transport
LMAN1, MCFD2
 GO:0016192 2 / 326 28.7× 1.78e-3 2.00e-2 ✓ sig.
protein exit from endoplasmic reticulum
LMAN1
 GO:0032527 1 / 14 334× 2.99e-3 2.59e-2 ✓ sig.
early endosome to Golgi transport
LMAN1
 GO:0034498 1 / 17 275× 3.63e-3 2.86e-2 ✓ sig.
phosphatidylinositol-mediated signaling
PI4KA
 GO:0048015 1 / 24 195× 5.13e-3 3.37e-2 ✓ sig.
protein transport
LMAN1, MCFD2
 GO:0015031 2 / 667 14.0× 7.28e-3 3.99e-2 ✓ sig.
phosphatidylinositol biosynthetic process
PI4KA
 GO:0006661 1 / 44 106× 9.39e-3 4.50e-2 ✓ sig.
endoplasmic reticulum organization
LMAN1
 GO:0007029 1 / 46 102× 9.81e-3 4.61e-2 ✓ sig.
intracellular iron ion homeostasis
TTC7A
 GO:0006879 1 / 71 65.8× 1.51e-2 5.68e-2
hemopoiesis
TTC7A
 GO:0030097 1 / 89 52.5× 1.89e-2 6.34e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Combined immunodeficiency, enteropathy spectrum Gastrointestinal defects and immunodeficiency syndrome 0.750 3 1.62e-12 1.71e-11 ✓ sig.
Intestinal atresia, inflammatory bowel disease and immunodeficiency Multiple intestinal atresia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Combined immunodeficiency, enteropathy spectrum Multiple intestinal atresia 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Combined immunodeficiency, enteropathy spectrum Intestinal atresia, inflammatory bowel disease and immunodeficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gastrointestinal defects and immunodeficiency syndrome Multiple intestinal atresia 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Gastrointestinal defects and immunodeficiency syndrome Intestinal atresia, inflammatory bowel disease and immunodeficiency 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Combined factor v and factor viii deficiency Combined immunodeficiency, enteropathy spectrum 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Combined factor v and factor viii deficiency Gastrointestinal defects and immunodeficiency syndrome 0.200 1 3.87e-4 7.33e-4 ✓ sig.