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 10
28
Diseases
178
Unique genes
0.025
Avg. similarity score
Immunodeficiency
Most-connected disease (21 links)
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.
Immunodeficiency
Severe combined immunodeficiency
Combined immunodeficiency disease
combined immunodeficiency due to CD3gamma deficiency
combined immunodeficiency due to STK4 deficiency
severe combined immunodeficiency due to CARMIL2 deficiency
severe combined immunodeficiency due to CTPS1 deficiency
severe combined immunodeficiency due to LCK deficiency
combined immunodeficiency due to GINS1 deficiency
combined immunodeficiency due to LRBA deficiency
combined immunodeficiency due to OX40 deficiency
combined immunodeficiency due to moesin deficiency
immunodeficiency 18
immunodeficiency 19
immunodeficiency 23
immunodeficiency 53
t-cell immunodeficiency, congenital alopecia, and nail dystrophy
Interferon gamma receptor deficiency
T-B+ severe combined immunodeficiency due to JAK3 deficiency
autosomal dominant combined immunodeficiency due to ERBIN deficiency
immunodeficiency 65, susceptibility to viral infections
immunodeficiency 80 with or without congenital cardiomyopathy
immunodeficiency 81
immunodeficiency 87 and autoimmunity
immunodeficiency 96
non-severe combined immunodeficiency due to COPG1 deficiency
purine nucleoside phosphorylase deficiency
reticular dysgenesis
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CARMIL2 | 4 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency, severe combined immunodeficiency due to CARMIL2 deficiency |
| CD3G | 4 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to CD3gamma deficiency, Immunodeficiency, Severe combined immunodeficiency |
| CTPS1 | 4 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency, severe combined immunodeficiency due to CTPS1 deficiency |
| LCK | 4 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency, severe combined immunodeficiency due to LCK deficiency |
| STK4 | 4 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to STK4 deficiency, Immunodeficiency, Severe combined immunodeficiency |
| CARD11 | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency |
| CD3D | 3 / 28 | Immunodeficiency, immunodeficiency 19, Severe combined immunodeficiency |
| CD3E | 3 / 28 | Immunodeficiency, immunodeficiency 18, Severe combined immunodeficiency |
| FOXN1 | 3 / 28 | Combined immunodeficiency disease, Severe combined immunodeficiency, t-cell immunodeficiency, congenital alopecia, and nail dystrophy |
| GINS1 | 3 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to GINS1 deficiency, Immunodeficiency |
| IKBKB | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency |
| LRBA | 3 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to LRBA deficiency, Severe combined immunodeficiency |
| MALT1 | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency |
| MSN | 3 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to moesin deficiency, Immunodeficiency |
| PGM3 | 3 / 28 | Immunodeficiency, immunodeficiency 23, Severe combined immunodeficiency |
| RELB | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, immunodeficiency 53 |
| TFRC | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency |
| TNFRSF4 | 3 / 28 | Combined immunodeficiency disease, combined immunodeficiency due to OX40 deficiency, Immunodeficiency |
| ZAP70 | 3 / 28 | Combined immunodeficiency disease, Immunodeficiency, Severe combined immunodeficiency |
| AK2 | 2 / 28 | reticular dysgenesis, Severe combined immunodeficiency |
| ARPC1B | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| BCL11B | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| CD247 | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| CD70 | 2 / 28 | Combined immunodeficiency disease, Severe combined immunodeficiency |
| COPG1 | 2 / 28 | Immunodeficiency, non-severe combined immunodeficiency due to COPG1 deficiency |
| CORO1A | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| DEF6 | 2 / 28 | Immunodeficiency, immunodeficiency 87 and autoimmunity |
| DOCK2 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| DOCK8 | 2 / 28 | Combined immunodeficiency disease, Severe combined immunodeficiency |
| DOP1A | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| ERBIN | 2 / 28 | autosomal dominant combined immunodeficiency due to ERBIN deficiency, Combined immunodeficiency disease |
| FCHO1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| ICOSLG | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| IFNGR1 | 2 / 28 | Immunodeficiency, Interferon gamma receptor deficiency |
| IFNGR2 | 2 / 28 | Immunodeficiency, Interferon gamma receptor deficiency |
| IL21R | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| IL2RG | 2 / 28 | Combined immunodeficiency disease, Severe combined immunodeficiency |
| IL6ST | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| IL7R | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| IRF4 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| IRF9 | 2 / 28 | Immunodeficiency, immunodeficiency 65, susceptibility to viral infections |
| JAK3 | 2 / 28 | Severe combined immunodeficiency, T-B+ severe combined immunodeficiency due to JAK3 deficiency |
| LAT | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| LCP2 | 2 / 28 | Immunodeficiency, immunodeficiency 81 |
| LIG1 | 2 / 28 | Immunodeficiency, immunodeficiency 96 |
| MCM10 | 2 / 28 | Immunodeficiency, immunodeficiency 80 with or without congenital cardiomyopathy |
| MST1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| NHEJ1 | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| ORAI1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| PNP | 2 / 28 | purine nucleoside phosphorylase deficiency, Severe combined immunodeficiency |
| POLD1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| PRKDC | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| PTPRC | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| RAG1 | 2 / 28 | Combined immunodeficiency disease, Severe combined immunodeficiency |
| RAG2 | 2 / 28 | Immunodeficiency, Severe combined immunodeficiency |
| REL | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| SLC19A1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| STIM1 | 2 / 28 | Combined immunodeficiency disease, Immunodeficiency |
| TMEM50B | 2 / 28 | Immunodeficiency, Interferon gamma receptor 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 ⇵ |
|---|---|---|---|---|---|
| Th17 cell differentiation | KEGG | 27 / 109 | 16.7× | 5.41e-26 | 1.13e-22 ✓ sig. |
| Measles | KEGG | 29 / 139 | 14.1× | 1.51e-25 | 2.92e-22 ✓ sig. |
| Primary immunodeficiency | KEGG | 19 / 38 | 33.7× | 1.84e-25 | 3.44e-22 ✓ sig. |
| T cell receptor signaling pathway | KEGG | 26 / 122 | 14.4× | 3.16e-23 | 4.36e-20 ✓ sig. |
| Th1 and Th2 cell differentiation | KEGG | 23 / 93 | 16.7× | 3.07e-22 | 3.72e-19 ✓ sig. |
| Herpes simplex virus 1 infection | KEGG | 29 / 182 | 10.8× | 4.85e-22 | 5.64e-19 ✓ sig. |
| Epstein-Barr virus infection | KEGG | 30 / 204 | 9.9× | 9.85e-22 | 1.05e-18 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 20 / 90 | 15.0× | 1.84e-18 | 1.17e-15 ✓ sig. |
| Influenza A | KEGG | 25 / 173 | 9.8× | 4.86e-18 | 2.82e-15 ✓ sig. |
| Toll-like receptor signaling pathway | KEGG | 21 / 109 | 13.0× | 5.80e-18 | 3.29e-15 ✓ sig. |
| Osteoclast differentiation | KEGG | 23 / 142 | 10.9× | 8.31e-18 | 4.59e-15 ✓ sig. |
| NF-kappa B signaling pathway | KEGG | 19 / 105 | 12.2× | 8.14e-16 | 3.19e-13 ✓ sig. |
| NOD-like receptor signaling pathway | KEGG | 23 / 187 | 8.3× | 4.26e-15 | 1.46e-12 ✓ sig. |
| JAK-STAT signaling pathway | KEGG | 22 / 168 | 8.8× | 4.61e-15 | 1.57e-12 ✓ sig. |
| Chagas disease | KEGG | 18 / 103 | 11.8× | 9.21e-15 | 2.91e-12 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| T cell activation | GO:0042110 | 22 / 76 | 30.4× | 4.23e-27 | 1.72e-23 ✓ sig. |
| immune system process | GO:0002376 | 53 / 943 | 5.9× | 8.31e-27 | 3.13e-23 ✓ sig. |
| T cell receptor signaling pathway | GO:0050852 | 22 / 121 | 19.1× | 3.12e-22 | 6.83e-19 ✓ sig. |
| T cell proliferation | GO:0042098 | 15 / 51 | 30.9× | 6.27e-19 | 8.57e-16 ✓ sig. |
| defense response to virus | GO:0051607 | 24 / 247 | 10.2× | 1.42e-17 | 1.60e-14 ✓ sig. |
| positive regulation of T cell proliferation | GO:0042102 | 15 / 67 | 23.5× | 5.96e-17 | 5.99e-14 ✓ sig. |
| cell surface receptor signaling pathway | GO:0007166 | 27 / 373 | 7.6× | 2.14e-16 | 1.90e-13 ✓ sig. |
| response to virus | GO:0009615 | 18 / 128 | 14.8× | 2.67e-16 | 2.33e-13 ✓ sig. |
| innate immune response | GO:0045087 | 33 / 605 | 5.7× | 3.22e-16 | 2.78e-13 ✓ sig. |
| positive regulation of canonical NF-kappaB signal transduction | GO:0043123 | 22 / 232 | 10.0× | 5.78e-16 | 4.74e-13 ✓ sig. |
| B cell differentiation | GO:0030183 | 15 / 80 | 19.7× | 1.03e-15 | 7.91e-13 ✓ sig. |
| T cell differentiation | GO:0030217 | 13 / 54 | 25.3× | 2.69e-15 | 1.96e-12 ✓ sig. |
| positive regulation of tumor necrosis factor production | GO:0032760 | 16 / 113 | 14.9× | 1.15e-14 | 7.43e-12 ✓ sig. |
| cytokine-mediated signaling pathway | GO:0019221 | 17 / 145 | 12.3× | 4.12e-14 | 2.42e-11 ✓ sig. |
| immune response | GO:0006955 | 28 / 543 | 5.4× | 2.92e-13 | 1.49e-10 ✓ sig. |