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 128

10 diseases · 19 shared-gene connections
10 Diseases
26 Unique genes
0.288 Avg. similarity score
Bare lymphocyte syndrome Most-connected disease (6 links)
Log in to save this analysis

Save This Analysis

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 ⇵
Bare lymphocyte syndrome 6 6 8
Visceral amyloidosis 6 6 4
Beta2-microglobulinic amyloidosis 5 5 1
Hypergammaglobulinemia 5 5 1
amyloidosis, hereditary systemic 6 5 5 1
hypoproteinemia, hypercatabolic 5 5 1
Alys amyloidosis 2 2 1
Amyloidosis 2 2 19
MHC class I deficiency 1 1 3
MHC class II deficiency 1 1 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
B2M 7 / 10 Amyloidosis, amyloidosis, hereditary systemic 6, Bare lymphocyte syndrome, Beta2-microglobulinic amyloidosis and 3 more
LYZ 3 / 10 Alys amyloidosis, Amyloidosis, Visceral amyloidosis
APOA1 2 / 10 Amyloidosis, Visceral amyloidosis
CIITA 2 / 10 Bare lymphocyte syndrome, MHC class II deficiency
FGA 2 / 10 Amyloidosis, Visceral amyloidosis
RFX5 2 / 10 Bare lymphocyte syndrome, MHC class II deficiency
RFXANK 2 / 10 Bare lymphocyte syndrome, MHC class II deficiency
RFXAP 2 / 10 Bare lymphocyte syndrome, MHC class II deficiency
TAP1 2 / 10 Bare lymphocyte syndrome, MHC class I deficiency
TAP2 2 / 10 Bare lymphocyte syndrome, MHC class I deficiency
TAPBP 2 / 10 Bare lymphocyte syndrome, MHC class I 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 ⇵
Antigen processing and presentation
B2M, CIITA, RFX5, RFXANK, RFXAP, TAP1, TAP2, TAPBP
 KEGG 8 / 81 45.6× 4.26e-12 8.17e-10 ✓ sig.
Amyloid fiber formation
FGA, LYZ, APCS, APP, GSN, TTR, APOA1, B2M
 Reactome 8 / 109 33.9× 4.84e-11 7.48e-9 ✓ sig.
Primary immunodeficiency
CIITA, RFX5, RFXANK, RFXAP, TAP1, TAP2
 KEGG 6 / 38 72.9× 1.46e-10 2.04e-8 ✓ sig.
Antigen Presentation: Folding, assembly and peptide loading of class I MHC
B2M, TAP1, TAP2, TAPBP
 Reactome 4 / 25 73.9× 2.12e-7 1.25e-5 ✓ sig.
ER-Phagosome pathway
B2M, TAP1, TAP2, TAPBP
 Reactome 4 / 30 61.6× 4.55e-7 2.47e-5 ✓ sig.
Post-translational protein phosphorylation
FGA, APOE, APP, APOA1
 Reactome 4 / 108 17.1× 7.94e-5 1.86e-3 ✓ sig.
Retinoid metabolism and transport
APOE, TTR, APOA1
 Reactome 3 / 41 33.8× 9.09e-5 2.08e-3 ✓ sig.
Platelet degranulation
FGA, APP, SERPINE1, APOA1
 Reactome 4 / 123 15.0× 1.32e-4 2.80e-3 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
FGA, APOE, APP, APOA1
 Reactome 4 / 125 14.8× 1.40e-4 2.94e-3 ✓ sig.
Chylomicron remodeling
APOE, APOA1
 Reactome 2 / 9 103× 1.61e-4 3.29e-3 ✓ sig.
Chylomicron assembly
APOE, APOA1
 Reactome 2 / 9 103× 1.61e-4 3.29e-3 ✓ sig.
HDL remodeling
APOE, APOA1
 Reactome 2 / 10 92.4× 2.01e-4 3.91e-3 ✓ sig.
Scavenging by Class A Receptors
APOE, APOA1
 Reactome 2 / 11 84.0× 2.45e-4 4.58e-3 ✓ sig.
Neutrophil degranulation
LYZ, DSP, GSN, PSEN1, TTR, B2M
 Reactome 6 / 480 5.8× 4.59e-4 7.46e-3 ✓ sig.
Tuberculosis
CIITA, RFX5, RFXANK, RFXAP
 KEGG 4 / 181 10.2× 5.76e-4 8.89e-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 ⇵
peptide antigen assembly with MHC class I protein complex
B2M, TAP1, TAP2, TAPBP
 GO:0002502 4 / 9 319× 3.69e-10 9.16e-8 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class I
B2M, TAP1, TAP2, TAPBP
 GO:0019885 4 / 9 319× 3.69e-10 9.16e-8 ✓ sig.
positive regulation of MHC class II biosynthetic process
CIITA, RFX5, RFXANK, RFXAP
 GO:0045348 4 / 15 192× 3.98e-9 7.61e-7 ✓ sig.
positive regulation of amyloid fibril formation
APOE, APP, PSEN1
 GO:1905908 3 / 5 431× 2.39e-8 3.64e-6 ✓ sig.
amyloid precursor protein metabolic process
ACHE, APOE, PSEN1
 GO:0042982 3 / 12 180× 5.22e-7 4.84e-5 ✓ sig.
cellular response to amyloid-beta
APOE, APP, PSEN1, APOA1
 GO:1904646 4 / 53 54.2× 8.23e-7 7.09e-5 ✓ sig.
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
B2M, TAP2
 GO:0002481 2 / 2 719× 1.86e-6 1.36e-4 ✓ sig.
cytosol to endoplasmic reticulum transport
TAP1, TAP2
 GO:0046967 2 / 2 719× 1.86e-6 1.36e-4 ✓ sig.
host-mediated suppression of symbiont invasion
APCS, GSN, CIITA
 GO:0046597 3 / 24 89.8× 4.75e-6 2.88e-4 ✓ sig.
regulation of amyloid-beta clearance
APOE, APP
 GO:1900221 2 / 3 479× 5.58e-6 3.27e-4 ✓ sig.
regulation of amyloid fibril formation
APOE, APP
 GO:1905906 2 / 3 479× 5.58e-6 3.27e-4 ✓ sig.
lipoprotein metabolic process
APOE, APP, APOA1
 GO:0042157 3 / 26 82.9× 6.09e-6 3.51e-4 ✓ sig.
amyloid fibril formation
APP, GSN, B2M
 GO:1990000 3 / 29 74.4× 8.53e-6 4.60e-4 ✓ sig.
positive regulation of phospholipid efflux
APOE, APOA1
 GO:1902995 2 / 4 359× 1.11e-5 5.66e-4 ✓ sig.
astrocyte activation involved in immune response
APP, PSEN1
 GO:0002265 2 / 4 359× 1.11e-5 5.66e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bare lymphocyte syndrome MHC class II deficiency 0.444 4 2.99e-14 4.26e-13 ✓ sig.
Amyloidosis Visceral amyloidosis 0.200 4 1.66e-12 2.05e-11 ✓ sig.
Bare lymphocyte syndrome MHC class I deficiency 0.333 3 9.21e-11 9.69e-10 ✓ sig.
amyloidosis, hereditary systemic 6 Beta2-microglobulinic amyloidosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
amyloidosis, hereditary systemic 6 Hypergammaglobulinemia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
amyloidosis, hereditary systemic 6 hypoproteinemia, hypercatabolic 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Hypergammaglobulinemia hypoproteinemia, hypercatabolic 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Beta2-microglobulinic amyloidosis Hypergammaglobulinemia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Beta2-microglobulinic amyloidosis hypoproteinemia, hypercatabolic 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Alys amyloidosis Visceral amyloidosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
amyloidosis, hereditary systemic 6 Visceral amyloidosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
hypoproteinemia, hypercatabolic Visceral amyloidosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Hypergammaglobulinemia Visceral amyloidosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Beta2-microglobulinic amyloidosis Visceral amyloidosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bare lymphocyte syndrome hypoproteinemia, hypercatabolic 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Bare lymphocyte syndrome Hypergammaglobulinemia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Bare lymphocyte syndrome Beta2-microglobulinic amyloidosis 0.111 1 5.20e-4 1.04e-3 ✓ sig.
amyloidosis, hereditary systemic 6 Bare lymphocyte syndrome 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Alys amyloidosis Amyloidosis 0.050 1 1.23e-3 1.97e-3 ✓ sig.