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 480

6 diseases · 11 shared-gene connections
6 Diseases
8 Unique genes
0.245 Avg. similarity score
Porokeratosis Most-connected disease (5 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 ⇵
Porokeratosis 5 5 8
Porokeratosis, multiple types 5 5 4
Disseminated superficial actinic porokeratosis 4 4 5
Porokeratosis 7, multiple types 3 3 1
Porokeratosis 9, multiple types 3 3 1
Porokeratosis 1, multiple types 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FDPS 4 / 6 Disseminated superficial actinic porokeratosis, Porokeratosis, Porokeratosis 9, multiple types, Porokeratosis, multiple types
MVD 4 / 6 Disseminated superficial actinic porokeratosis, Porokeratosis, Porokeratosis 7, multiple types, Porokeratosis, multiple types
MVK 3 / 6 Disseminated superficial actinic porokeratosis, Porokeratosis, Porokeratosis, multiple types
PMVK 3 / 6 Porokeratosis, Porokeratosis 1, multiple types, Porokeratosis, multiple types
SART3 2 / 6 Disseminated superficial actinic porokeratosis, Porokeratosis
SLC17A9 2 / 6 Disseminated superficial actinic porokeratosis, Porokeratosis
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 ⇵
Cholesterol biosynthesis
FDPS, MVD, MVK, PMVK
 Reactome 4 / 21 286× 4.81e-10 4.82e-8 ✓ sig.
Terpenoid backbone biosynthesis
FDPS, MVD, MVK, PMVK
 KEGG 4 / 23 261× 7.12e-10 6.82e-8 ✓ sig.
Activation of gene expression by SREBF (SREBP)
FDPS, MVD, MVK, PMVK
 Reactome 4 / 42 143× 8.95e-9 6.69e-7 ✓ sig.
Transport of connexons to the plasma membrane
GJB2
 Reactome 1 / 1 1,501× 6.66e-4 8.31e-3 ✓ sig.
Peroxisome
MVK, PMVK
 KEGG 2 / 83 36.2× 1.29e-3 1.37e-2 ✓ sig.
Synthesis of Dolichyl-phosphate
MVD
 Reactome 1 / 6 250× 3.99e-3 3.12e-2 ✓ sig.
Metabolic pathways
FDPS, MVD, MVK, PMVK
 KEGG 4 / 1,563 3.8× 1.29e-2 6.63e-2
Influenza A
FDPS
 KEGG 1 / 173 8.7× 1.10e-1 2.28e-1
Human T-cell leukemia virus 1 infection
FDPS
 KEGG 1 / 224 6.7× 1.40e-1 2.64e-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 ⇵
isopentenyl diphosphate biosynthetic process, mevalonate pathway
MVD, MVK, PMVK
 GO:0019287 3 / 3 2,336× 5.15e-11 1.69e-8 ✓ sig.
sterol biosynthetic process
FDPS, MVD, MVK, PMVK
 GO:0016126 4 / 31 301× 4.32e-10 1.13e-7 ✓ sig.
cholesterol biosynthetic process
FDPS, MVD, MVK, PMVK
 GO:0006695 4 / 39 240× 1.13e-9 2.57e-7 ✓ sig.
steroid biosynthetic process
FDPS, MVD, MVK, PMVK
 GO:0006694 4 / 65 144× 9.23e-9 1.65e-6 ✓ sig.
isoprenoid biosynthetic process
FDPS, MVD, MVK
 GO:0008299 3 / 13 539× 1.47e-8 2.47e-6 ✓ sig.
cholesterol metabolic process
FDPS, MVD, MVK, PMVK
 GO:0008203 4 / 107 87.3× 6.99e-8 9.43e-6 ✓ sig.
steroid metabolic process
FDPS, MVD, MVK, PMVK
 GO:0008202 4 / 135 69.2× 1.78e-7 2.05e-5 ✓ sig.
lipid metabolic process
FDPS, MVD, MVK, PMVK
 GO:0006629 4 / 840 11.1× 2.45e-4 5.87e-3 ✓ sig.
purine nucleotide import into lysosome
SLC17A9
 GO:0141013 1 / 1 2,336× 4.28e-4 8.53e-3 ✓ sig.
guanine nucleotide transmembrane transport
SLC17A9
 GO:1903790 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
geranyl diphosphate biosynthetic process
FDPS
 GO:0033384 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
farnesyl diphosphate biosynthetic process
FDPS
 GO:0045337 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
purine-containing compound transmembrane transport
SLC17A9
 GO:0072530 1 / 4 584× 1.71e-3 1.96e-2 ✓ sig.
gap junction-mediated intercellular transport
GJB2
 GO:1990349 1 / 6 389× 2.57e-3 2.40e-2 ✓ sig.
cell communication by electrical coupling
GJB2
 GO:0010644 1 / 7 334× 2.99e-3 2.59e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Disseminated superficial actinic porokeratosis Porokeratosis 0.556 5 7.55e-18 1.02e-16 ✓ sig.
Porokeratosis Porokeratosis, multiple types 0.444 4 2.92e-14 3.41e-13 ✓ sig.
Disseminated superficial actinic porokeratosis Porokeratosis, multiple types 0.429 3 6.46e-11 6.13e-10 ✓ sig.
Porokeratosis 1, multiple types Porokeratosis, multiple types 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Porokeratosis 7, multiple types Porokeratosis, multiple types 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Porokeratosis 9, multiple types Porokeratosis, multiple types 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Disseminated superficial actinic porokeratosis Porokeratosis 7, multiple types 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Disseminated superficial actinic porokeratosis Porokeratosis 9, multiple types 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Porokeratosis Porokeratosis 1, multiple types 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Porokeratosis Porokeratosis 7, multiple types 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Porokeratosis Porokeratosis 9, multiple types 0.111 1 5.17e-4 9.13e-4 ✓ sig.