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 425

5 diseases · 7 shared-gene connections
5 Diseases
10 Unique genes
0.169 Avg. similarity score
Pulmonary alveolar proteinosis 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 ⇵
Pulmonary alveolar proteinosis 4 4 9
Pulmonary surfactant metabolism dysfunction 4 4 6
surfactant metabolism dysfunction, pulmonary, 1 2 2 1
surfactant metabolism dysfunction, pulmonary, 4 2 2 1
surfactant metabolism dysfunction, pulmonary, 5 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CSF2RA 3 / 5 Pulmonary alveolar proteinosis, Pulmonary surfactant metabolism dysfunction, surfactant metabolism dysfunction, pulmonary, 4
CSF2RB 3 / 5 Pulmonary alveolar proteinosis, Pulmonary surfactant metabolism dysfunction, surfactant metabolism dysfunction, pulmonary, 5
SFTPB 3 / 5 Pulmonary alveolar proteinosis, Pulmonary surfactant metabolism dysfunction, surfactant metabolism dysfunction, pulmonary, 1
ABCA3 2 / 5 Pulmonary alveolar proteinosis, Pulmonary surfactant metabolism dysfunction
SFTPC 2 / 5 Pulmonary alveolar proteinosis, Pulmonary surfactant metabolism dysfunction
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 ⇵
Defective CSF2RB causes pulmonary surfactant metabolism dysfunction 5 (SMDP5)
CSF2RA, CSF2RB, SFTPB, SFTPC
 Reactome 4 / 7 686× 8.47e-12 1.54e-9 ✓ sig.
Defective CSF2RA causes pulmonary surfactant metabolism dysfunction 4 (SMDP4)
CSF2RA, CSF2RB, SFTPB, SFTPC
 Reactome 4 / 7 686× 8.47e-12 1.54e-9 ✓ sig.
Surfactant metabolism
ABCA3, CSF2RA, CSF2RB, SFTPB, SFTPC
 Reactome 5 / 29 207× 1.43e-11 2.46e-9 ✓ sig.
Interleukin-3, Interleukin-5 and GM-CSF signaling
CSF2, CSF2RA, CSF2RB
 Reactome 3 / 23 157× 7.30e-7 3.71e-5 ✓ sig.
Hematopoietic cell lineage
CSF2, CSF2RA, HLA-DRB5, HLA-DRB1
 KEGG 4 / 100 48.0× 9.14e-7 4.51e-5 ✓ sig.
Interleukin receptor SHC signaling
CSF2, CSF2RA, CSF2RB
 Reactome 3 / 27 133× 1.20e-6 5.74e-5 ✓ sig.
Interferon gamma signaling
HLA-DRB5, OAS1, HLA-DRB1
 Reactome 3 / 87 41.4× 4.25e-5 1.12e-3 ✓ sig.
Rheumatoid arthritis
CSF2, HLA-DRB5, HLA-DRB1
 KEGG 3 / 95 37.9× 5.53e-5 1.39e-3 ✓ sig.
Translocation of ZAP-70 to Immunological synapse
HLA-DRB5, HLA-DRB1
 Reactome 2 / 19 126× 1.06e-4 2.36e-3 ✓ sig.
RAF/MAP kinase cascade
CSF2, CSF2RA, CSF2RB
 Reactome 3 / 124 29.1× 1.22e-4 2.64e-3 ✓ sig.
Phosphorylation of CD3 and TCR zeta chains
HLA-DRB5, HLA-DRB1
 Reactome 2 / 22 109× 1.43e-4 2.99e-3 ✓ sig.
PD-1 signaling
HLA-DRB5, HLA-DRB1
 Reactome 2 / 23 104× 1.56e-4 3.21e-3 ✓ sig.
Generation of second messenger molecules
HLA-DRB5, HLA-DRB1
 Reactome 2 / 31 77.5× 2.86e-4 5.18e-3 ✓ sig.
JAK-STAT signaling pathway
CSF2, CSF2RA, CSF2RB
 KEGG 3 / 168 21.4× 3.00e-4 5.37e-3 ✓ sig.
Asthma
HLA-DRB5, HLA-DRB1
 KEGG 2 / 32 75.1× 3.05e-4 5.44e-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 ⇵
granulocyte-macrophage colony-stimulating factor signaling pathway
CSF2, CSF2RA, CSF2RB
 GO:0038157 3 / 4 1,402× 4.41e-10 1.07e-7 ✓ sig.
positive regulation of leukocyte proliferation
CSF2, CSF2RA, CSF2RB
 GO:0070665 3 / 6 934× 2.21e-9 4.50e-7 ✓ sig.
respiratory gaseous exchange by respiratory system
CSF2RB, SFTPB, SFTPC
 GO:0007585 3 / 31 181× 4.92e-7 4.62e-5 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT
CSF2, CSF2RA, CSF2RB
 GO:0007259 3 / 67 83.7× 5.19e-6 3.10e-4 ✓ sig.
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
HLA-DRB5, HLA-DRB1
 GO:0002504 2 / 15 249× 2.70e-5 1.13e-3 ✓ sig.
peptide antigen assembly with MHC class II protein complex
HLA-DRB5, HLA-DRB1
 GO:0002503 2 / 16 234× 3.08e-5 1.25e-3 ✓ sig.
surfactant homeostasis
ABCA3, OAS1
 GO:0043129 2 / 18 208× 3.93e-5 1.50e-3 ✓ sig.
antigen processing and presentation of exogenous peptide antigen via MHC class II
HLA-DRB5, HLA-DRB1
 GO:0019886 2 / 31 121× 1.19e-4 3.45e-3 ✓ sig.
macrophage differentiation
CSF2, HLA-DRB1
 GO:0030225 2 / 37 101× 1.70e-4 4.50e-3 ✓ sig.
positive regulation of immune response
HLA-DRB5, HLA-DRB1
 GO:0050778 2 / 40 93.4× 1.99e-4 5.03e-3 ✓ sig.
positive regulation of T cell activation
HLA-DRB5, HLA-DRB1
 GO:0050870 2 / 45 83.1× 2.52e-4 5.96e-3 ✓ sig.
antigen processing and presentation
HLA-DRB5, HLA-DRB1
 GO:0019882 2 / 48 77.9× 2.87e-4 6.50e-3 ✓ sig.
positive regulation of protein homooligomerization
ABCA3
 GO:0032464 1 / 1 1,869× 5.35e-4 9.98e-3 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class II
HLA-DRB1
 GO:0002491 1 / 2 934× 1.07e-3 1.57e-2 ✓ sig.
regulation of interleukin-10 production
HLA-DRB1
 GO:0032653 1 / 2 934× 1.07e-3 1.57e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pulmonary alveolar proteinosis Pulmonary surfactant metabolism dysfunction 0.455 5 1.05e-16 1.78e-15 ✓ sig.
Pulmonary surfactant metabolism dysfunction surfactant metabolism dysfunction, pulmonary, 5 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Pulmonary surfactant metabolism dysfunction surfactant metabolism dysfunction, pulmonary, 1 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Pulmonary surfactant metabolism dysfunction surfactant metabolism dysfunction, pulmonary, 4 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Pulmonary alveolar proteinosis surfactant metabolism dysfunction, pulmonary, 1 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Pulmonary alveolar proteinosis surfactant metabolism dysfunction, pulmonary, 4 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Pulmonary alveolar proteinosis surfactant metabolism dysfunction, pulmonary, 5 0.100 1 5.84e-4 1.14e-3 ✓ sig.