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 142
9
Diseases
392
Unique genes
0.121
Avg. similarity score
Common variable immunodeficiency
Most-connected disease (7 links)
Disease
Searched: immunodeficiency, common variable, 4
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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immunodeficiency, common variable, 4
Common variable immunodeficiency
Autoimmune disease
Autoimmune thyroid disease
Celiac disease
isolated sulfite oxidase deficiency
Autoinflammation with pulmonary and cutaneous vasculitis
immunodeficiency, common variable, 6
immunodeficiency, common variable, 7
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Common variable immunodeficiency | 7 | 7 | 75 |
| Autoimmune disease | 4 | 4 | 202 |
| Autoimmune thyroid disease | 4 | 4 | 144 |
| Celiac disease | 4 | 4 | 193 |
| isolated sulfite oxidase deficiency | 3 | 3 | 1 |
| Autoinflammation with pulmonary and cutaneous vasculitis | 1 | 1 | 1 |
| immunodeficiency, common variable, 4 | 1 | 1 | 1 |
| immunodeficiency, common variable, 6 | 1 | 1 | 1 |
| immunodeficiency, common variable, 7 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases ‐ top 100 shown, download for all)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SUOX | 5 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency and 1 more |
| ADCY7 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ADGRL2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ANKRD55 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ATG16L1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ATXN2L | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| C1ORF141 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| CARD9 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| CRB1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| CYTL1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| DAG1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| DCTD | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ERAP2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| FNBP1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| FUT2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| GPR35 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| GSDMB | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| HLA-DQB1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ICOS | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IGF2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IL10 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IL18RAP | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IL23R | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IL2RA | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| INS-IGF2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| IRF1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| JAK2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| KEAP1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| LRRK2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| LURAP1L | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| NKD1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| NKX2-3 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| NPIPB6 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| PDE4A | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| PHTF1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| RSBN1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| SBK1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| SLC25A28 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| SLC9A4 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| SMAD3 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| STMN3 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| TENM3 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| TNFSF15 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| TTC33 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ZMIZ1 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| ZPBP2 | 4 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease, Common variable immunodeficiency |
| BACH2 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| CTLA4 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| ELMO1 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| IRF4 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| LPP | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| MMEL1 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| PSMB9 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| PTPN2 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| SH2B3 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| STAT4 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| TNFRSF14 | 3 / 9 | Autoimmune disease, Autoimmune thyroid disease, Celiac disease |
| AFF3 | 2 / 9 | Autoimmune disease, Celiac disease |
| ARHGAP31 | 2 / 9 | Autoimmune disease, Celiac disease |
| ARID5B | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| ATXN2 | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| BANF2 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| BTNL2 | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| C12ORF42 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| C1QTNF6 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| CAMK4 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| CBLB | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| CCL21 | 2 / 9 | Autoimmune disease, Celiac disease |
| CCN4 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| CD226 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| CD247 | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| CD28 | 2 / 9 | Autoimmune disease, Celiac disease |
| CD40LG | 2 / 9 | Autoimmune disease, Common variable immunodeficiency |
| CD81 | 2 / 9 | Common variable immunodeficiency, immunodeficiency, common variable, 6 |
| CR2 | 2 / 9 | Common variable immunodeficiency, immunodeficiency, common variable, 7 |
| CTSH | 2 / 9 | Autoimmune disease, Celiac disease |
| CXCR5 | 2 / 9 | Autoimmune disease, Celiac disease |
| DNASE1L3 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| ERBB3 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| FAM76B | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| FASLG | 2 / 9 | Autoimmune disease, Celiac disease |
| FLT3 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| GIGYF1 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| HCK | 2 / 9 | Autoimmune disease, Autoinflammation with pulmonary and cutaneous vasculitis |
| HLA-B | 2 / 9 | Autoimmune disease, Celiac disease |
| HLA-DOA | 2 / 9 | Autoimmune disease, Celiac disease |
| HLA-DPA1 | 2 / 9 | Autoimmune disease, Celiac disease |
| HLA-DQA1 | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| HLA-DRA | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| HLA-DRB1 | 2 / 9 | Autoimmune thyroid disease, Celiac disease |
| IFNG | 2 / 9 | Autoimmune disease, Celiac disease |
| IKZF1 | 2 / 9 | Autoimmune disease, Common variable immunodeficiency |
| IL21 | 2 / 9 | Celiac disease, Common variable immunodeficiency |
| IL6 | 2 / 9 | Autoimmune disease, Celiac disease |
| JAK1 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| MACIR | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| MBL2 | 2 / 9 | Autoimmune thyroid disease, Common variable immunodeficiency |
| PLEKHA1 | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| PPARG | 2 / 9 | Autoimmune disease, Autoimmune thyroid disease |
| PRRC2A | 2 / 9 | Autoimmune disease, Celiac disease |
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 ⇵ |
|---|---|---|---|---|---|
| Intestinal immune network for IgA production | KEGG | 26 / 50 | 15.9× | 5.95e-26 | 1.14e-22 ✓ sig. |
| Inflammatory bowel disease | KEGG | 28 / 66 | 13.0× | 1.03e-24 | 1.60e-21 ✓ sig. |
| Th17 cell differentiation | KEGG | 32 / 109 | 9.0× | 3.01e-22 | 3.28e-19 ✓ sig. |
| Autoimmune thyroid disease | KEGG | 24 / 54 | 13.6× | 6.09e-22 | 6.04e-19 ✓ sig. |
| Allograft rejection | KEGG | 21 / 39 | 16.5× | 1.32e-21 | 1.17e-18 ✓ sig. |
| Graft-versus-host disease | KEGG | 19 / 45 | 12.9× | 4.20e-17 | 1.80e-14 ✓ sig. |
| Th1 and Th2 cell differentiation | KEGG | 25 / 93 | 8.2× | 1.29e-16 | 5.15e-14 ✓ sig. |
| Type I diabetes mellitus | KEGG | 18 / 44 | 12.5× | 5.69e-16 | 2.08e-13 ✓ sig. |
| Cytokine-cytokine receptor interaction | KEGG | 41 / 298 | 4.2× | 3.54e-15 | 1.13e-12 ✓ sig. |
| Herpes simplex virus 1 infection | KEGG | 31 / 182 | 5.2× | 2.71e-14 | 7.27e-12 ✓ sig. |
| Toxoplasmosis | KEGG | 24 / 112 | 6.6× | 1.31e-13 | 3.12e-11 ✓ sig. |
| Primary immunodeficiency | KEGG | 15 / 38 | 12.1× | 3.04e-13 | 6.78e-11 ✓ sig. |
| Interferon gamma signaling | Reactome | 21 / 87 | 7.4× | 3.79e-13 | 8.24e-11 ✓ sig. |
| Rheumatoid arthritis | KEGG | 21 / 95 | 6.8× | 2.41e-12 | 4.57e-10 ✓ sig. |
| Epstein-Barr virus infection | KEGG | 30 / 204 | 4.5× | 3.74e-12 | 6.89e-10 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| immune response | GO:0006955 | 72 / 543 | 6.3× | 4.39e-37 | 3.74e-33 ✓ sig. |
| immune system process | GO:0002376 | 86 / 943 | 4.3× | 6.64e-32 | 3.93e-28 ✓ sig. |
| positive regulation of T cell proliferation | GO:0042102 | 20 / 67 | 14.2× | 3.96e-18 | 4.78e-15 ✓ sig. |
| inflammatory response | GO:0006954 | 45 / 467 | 4.6× | 1.13e-17 | 1.24e-14 ✓ sig. |
| adaptive immune response | GO:0002250 | 45 / 507 | 4.2× | 2.57e-16 | 2.18e-13 ✓ sig. |
| peptide antigen assembly with MHC class II protein complex | GO:0002503 | 11 / 16 | 32.8× | 1.20e-15 | 8.86e-13 ✓ sig. |
| antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | GO:0002504 | 10 / 15 | 31.8× | 4.03e-14 | 2.32e-11 ✓ sig. |
| cell surface receptor signaling pathway | GO:0007166 | 35 / 373 | 4.5× | 1.26e-13 | 6.71e-11 ✓ sig. |
| positive regulation of T cell activation | GO:0050870 | 14 / 45 | 14.8× | 2.35e-13 | 1.19e-10 ✓ sig. |
| antigen processing and presentation of exogenous peptide antigen via MHC class II | GO:0019886 | 12 / 31 | 18.5× | 6.05e-13 | 2.82e-10 ✓ sig. |
| positive regulation of immune response | GO:0050778 | 13 / 40 | 15.5× | 9.01e-13 | 4.08e-10 ✓ sig. |
| antigen processing and presentation | GO:0019882 | 13 / 48 | 12.9× | 1.24e-11 | 4.40e-9 ✓ sig. |
| positive regulation of tumor necrosis factor production | GO:0032760 | 18 / 113 | 7.6× | 2.29e-11 | 7.64e-9 ✓ sig. |
| cellular response to lipopolysaccharide | GO:0071222 | 22 / 187 | 5.6× | 6.63e-11 | 1.96e-8 ✓ sig. |
| T cell receptor signaling pathway | GO:0050852 | 18 / 121 | 7.1× | 7.45e-11 | 2.17e-8 ✓ sig. |