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 155
9
Diseases
18
Unique genes
0.214
Avg. similarity score
Leukocyte disorders
Most-connected disease (7 links)
Disease
Searched: Developmental delay with autism spectrum disorder
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Developmental delay with autism spectrum disorder
Leukocyte disorders
Conjunctivitis
hypoplasminogenemia
Laryngeal disease
Splenic disease
Congenital leukocyte adherence deficiency
FAS-related autoimmune lymphoproliferative immune disorder
Leukocyte adhesion deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Leukocyte disorders | 7 | 7 | 3 |
| Conjunctivitis | 4 | 4 | 2 |
| hypoplasminogenemia | 4 | 4 | 1 |
| Laryngeal disease | 3 | 3 | 6 |
| Splenic disease | 3 | 3 | 9 |
| Congenital leukocyte adherence deficiency | 2 | 2 | 2 |
| FAS-related autoimmune lymphoproliferative immune disorder | 2 | 2 | 1 |
| Leukocyte adhesion deficiency | 2 | 2 | 3 |
| Developmental delay with autism spectrum disorder | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PLG | 5 / 9 | Conjunctivitis, hypoplasminogenemia, Laryngeal disease, Leukocyte disorders and 1 more |
| FAS | 3 / 9 | FAS-related autoimmune lymphoproliferative immune disorder, Leukocyte disorders, Splenic disease |
| ITGB2 | 3 / 9 | Congenital leukocyte adherence deficiency, Leukocyte adhesion deficiency, Leukocyte disorders |
| FERMT3 | 2 / 9 | Congenital leukocyte adherence deficiency, Leukocyte adhesion deficiency |
| HERC2 | 2 / 9 | Conjunctivitis, Developmental delay with autism spectrum disorder |
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 ⇵ |
|---|---|---|---|---|---|
| Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 | Reactome | 1 / 1 | 667× | 1.50e-3 | 1.92e-2 ✓ sig. |
| APC truncation mutants are not K63 polyubiquitinated | Reactome | 1 / 1 | 667× | 1.50e-3 | 1.92e-2 ✓ sig. |
| Defective SLC35C1 causes congenital disorder of glycosylation 2C (CDG2C) | Reactome | 1 / 1 | 667× | 1.50e-3 | 1.92e-2 ✓ sig. |
| Influenza A | KEGG | 3 / 173 | 11.6× | 2.04e-3 | 2.41e-2 ✓ sig. |
| Chemical carcinogenesis - receptor activation | KEGG | 3 / 215 | 9.3× | 3.79e-3 | 3.73e-2 ✓ sig. |
| Leishmaniasis | KEGG | 2 / 78 | 17.1× | 5.96e-3 | 5.10e-2 |
| Biosynthesis of protectins | Reactome | 1 / 4 | 167× | 5.98e-3 | 5.11e-2 |
| FasL/ CD95L signaling | Reactome | 1 / 5 | 133× | 7.47e-3 | 5.89e-2 |
| Complement and coagulation cascades | KEGG | 2 / 88 | 15.2× | 7.53e-3 | 5.91e-2 |
| Caffeine metabolism | KEGG | 1 / 6 | 111× | 8.96e-3 | 6.62e-2 |
| Biosynthesis of maresin-like SPMs | Reactome | 1 / 6 | 111× | 8.96e-3 | 6.62e-2 |
| GDP-fucose biosynthesis | Reactome | 1 / 6 | 111× | 8.96e-3 | 6.62e-2 |
| Staphylococcus aureus infection | KEGG | 2 / 99 | 13.5× | 9.44e-3 | 6.85e-2 |
| Aryl hydrocarbon receptor signalling | Reactome | 1 / 7 | 95.3× | 1.04e-2 | 7.29e-2 |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 2 / 108 | 12.4× | 1.12e-2 | 7.59e-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 ⇵ |
|---|---|---|---|---|---|
| cell adhesion | GO:0007155 | 6 / 665 | 9.4× | 2.56e-5 | 1.11e-3 ✓ sig. |
| proteasome-mediated ubiquitin-dependent protein catabolic process | GO:0043161 | 4 / 343 | 12.1× | 2.78e-4 | 6.58e-3 ✓ sig. |
| microglial cell activation | GO:0001774 | 2 / 28 | 74.2× | 3.26e-4 | 7.35e-3 ✓ sig. |
| leukocyte cell-cell adhesion | GO:0007159 | 2 / 33 | 62.9× | 4.55e-4 | 9.28e-3 ✓ sig. |
| positive regulation of apoptotic signaling pathway | GO:2001235 | 2 / 37 | 56.1× | 5.72e-4 | 1.08e-2 ✓ sig. |
| positive regulation of nitric oxide biosynthetic process | GO:0045429 | 2 / 42 | 49.4× | 7.37e-4 | 1.29e-2 ✓ sig. |
| negative regulation of Notch signaling pathway | GO:0045746 | 2 / 42 | 49.4× | 7.37e-4 | 1.29e-2 ✓ sig. |
| toxin biosynthetic process | GO:0009403 | 1 / 1 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| GDP-fucose import into Golgi lumen | GO:0036085 | 1 / 1 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| nuclear receptor-mediated mineralocorticoid signaling pathway | GO:0031959 | 1 / 1 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| symbiont-induced defense-related programmed cell death | GO:0034050 | 1 / 1 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| interleukin-35-mediated signaling pathway | GO:0070757 | 1 / 1 | 1,038× | 9.63e-4 | 1.52e-2 ✓ sig. |
| cell-cell adhesion | GO:0098609 | 3 / 218 | 14.3× | 1.12e-3 | 1.68e-2 ✓ sig. |
| extrinsic apoptotic signaling pathway | GO:0097191 | 2 / 57 | 36.4× | 1.36e-3 | 1.87e-2 ✓ sig. |
| tumor necrosis factor-mediated signaling pathway | GO:0033209 | 2 / 60 | 34.6× | 1.50e-3 | 1.99e-2 ✓ sig. |