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.

← Back to all clusters

Cluster 179

10 diseases · 25 shared-gene connections
10 Diseases
10 Unique genes
0.319 Avg. similarity score
Hyper-igd syndrome Most-connected disease (7 links)
Log in to save this analysis

Save This Analysis

Disease Searched: Porokeratosis 3, multiple types 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 ⇵
Hyper-igd syndrome 7 7 1
Hyperimmunoglobulinemia d and periodic fever syndrome 7 7 1
Mevalonic aciduria 7 7 1
Porokeratosis 3, multiple types 7 7 1
Hyper-immunoglobulin d syndrome 6 6 4
Arthralgia 5 5 2
Mevalonate kinase deficiency 5 5 2
Exanthema 4 4 6
Bone marrow neoplasms 1 1 1
Methylmalonic aciduria, cblb type 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MVK 8 / 10 Arthralgia, Exanthema, Hyper-igd syndrome, Hyper-immunoglobulin d syndrome and 4 more
CSF3 2 / 10 Arthralgia, Bone marrow neoplasms
HMGCR 2 / 10 Hyper-immunoglobulin d syndrome, Mevalonate kinase deficiency
MMAB 2 / 10 Hyper-immunoglobulin d syndrome, Methylmalonic aciduria, cblb type
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
MVK, HMGCR
 Reactome 2 / 21 114× 1.30e-4 2.33e-3 ✓ sig.
Terpenoid backbone biosynthesis
MVK, HMGCR
 KEGG 2 / 23 104× 1.56e-4 2.70e-3 ✓ sig.
Activation of gene expression by SREBF (SREBP)
MVK, HMGCR
 Reactome 2 / 42 57.2× 5.28e-4 6.96e-3 ✓ sig.
Interleukin-10 signaling
CSF3, IL1RN
 Reactome 2 / 47 51.1× 6.61e-4 8.28e-3 ✓ sig.
Coronavirus disease - COVID-19
CSF3, C1QA, VWF
 KEGG 3 / 238 15.1× 8.32e-4 9.85e-3 ✓ sig.
Defective MMAB causes methylmalonic aciduria type cblB
MMAB
 Reactome 1 / 1 1,201× 8.33e-4 9.85e-3 ✓ sig.
Transfer of LPS from LBP carrier to CD14
LBP
 Reactome 1 / 2 601× 1.66e-3 1.66e-2 ✓ sig.
Complement and coagulation cascades
C1QA, VWF
 KEGG 2 / 88 27.3× 2.30e-3 2.11e-2 ✓ sig.
Classical antibody-mediated complement activation
C1QA
 Reactome 1 / 6 200× 4.99e-3 3.64e-2 ✓ sig.
Alcoholic liver disease
C1QA, LBP
 KEGG 2 / 144 16.7× 6.03e-3 4.12e-2 ✓ sig.
Platelet Aggregation (Plug Formation)
VWF
 Reactome 1 / 8 150× 6.64e-3 4.39e-2 ✓ sig.
Endosomal/Vacuolar pathway
HLA-B
 Reactome 1 / 8 150× 6.64e-3 4.39e-2 ✓ sig.
Efferocytosis
C1QA, VPS41
 KEGG 2 / 157 15.3× 7.13e-3 4.60e-2 ✓ sig.
Platelet Adhesion to exposed collagen
VWF
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
GP1b-IX-V activation signalling
VWF
 Reactome 1 / 12 100× 9.95e-3 5.67e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
isoprenoid biosynthetic process
MVK, HMGCR
 GO:0008299 2 / 13 287× 2.00e-5 9.25e-4 ✓ sig.
sterol biosynthetic process
MVK, HMGCR
 GO:0016126 2 / 31 121× 1.19e-4 3.50e-3 ✓ sig.
acute-phase response
IL1RN, LBP
 GO:0006953 2 / 37 101× 1.70e-4 4.51e-3 ✓ sig.
cholesterol biosynthetic process
MVK, HMGCR
 GO:0006695 2 / 39 95.8× 1.89e-4 4.89e-3 ✓ sig.
steroid biosynthetic process
MVK, HMGCR
 GO:0006694 2 / 65 57.5× 5.27e-4 9.87e-3 ✓ sig.
lipopolysaccharide transport
LBP
 GO:0015920 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
positive regulation of respiratory burst involved in inflammatory response
LBP
 GO:0060265 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
cholesterol metabolic process
MVK, HMGCR
 GO:0008203 2 / 107 34.9× 1.42e-3 1.78e-2 ✓ sig.
isopentenyl diphosphate biosynthetic process, mevalonate pathway
MVK
 GO:0019287 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
vertebrate eye-specific patterning
C1QA
 GO:0150064 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
detection of molecule of bacterial origin
LBP
 GO:0032490 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
regulation of interleukin-12 production
HLA-B
 GO:0032655 1 / 4 467× 2.14e-3 2.19e-2 ✓ sig.
regulation of dendritic cell differentiation
HLA-B
 GO:2001198 1 / 4 467× 2.14e-3 2.19e-2 ✓ sig.
complement-mediated synapse pruning
C1QA
 GO:0150062 1 / 4 467× 2.14e-3 2.19e-2 ✓ sig.
regulation of T cell anergy
HLA-B
 GO:0002667 1 / 4 467× 2.14e-3 2.19e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyper-immunoglobulin d syndrome Mevalonate kinase deficiency 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Mevalonic aciduria Porokeratosis 3, multiple types 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyperimmunoglobulinemia d and periodic fever syndrome Mevalonic aciduria 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyperimmunoglobulinemia d and periodic fever syndrome Porokeratosis 3, multiple types 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper-igd syndrome Porokeratosis 3, multiple types 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper-igd syndrome Mevalonic aciduria 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper-igd syndrome Hyperimmunoglobulinemia d and periodic fever syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyper-igd syndrome Mevalonate kinase deficiency 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mevalonate kinase deficiency Mevalonic aciduria 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Mevalonate kinase deficiency Porokeratosis 3, multiple types 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hyperimmunoglobulinemia d and periodic fever syndrome Mevalonate kinase deficiency 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arthralgia Hyper-igd syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arthralgia Bone marrow neoplasms 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arthralgia Hyperimmunoglobulinemia d and periodic fever syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arthralgia Mevalonic aciduria 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Arthralgia Porokeratosis 3, multiple types 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hyper-igd syndrome Hyper-immunoglobulin d syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hyper-immunoglobulin d syndrome Porokeratosis 3, multiple types 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hyper-immunoglobulin d syndrome Mevalonic aciduria 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hyper-immunoglobulin d syndrome Hyperimmunoglobulinemia d and periodic fever syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Hyper-immunoglobulin d syndrome Methylmalonic aciduria, cblb type 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Exanthema Hyperimmunoglobulinemia d and periodic fever syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Exanthema Mevalonic aciduria 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Exanthema Porokeratosis 3, multiple types 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Exanthema Hyper-igd syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.