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 21
24
Diseases
197
Unique genes
0.113
Avg. similarity score
Immunodeficiency
Most-connected disease (14 links)
Disease
Searched: Immunodeficiency 87 and autoimmunity
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Immunodeficiency 87 and autoimmunity
Immunodeficiency
Severe combined immunodeficiency
Combined immunodeficiency
T-B+ severe combined immunodeficiency
Lig4 syndrome
Omenn syndrome
Severe combined immunodeficiency autosomal recessive t-cell-negative/b-cell-negative/nk-cell-positive with sensitivity to ionizing radiation
Acute lymphoblastic leukemia
Dna ligase iv deficiency
Dubowitz syndrome
Immunodeficiency 17, cd3 gamma deficient
Immunodeficiency 18
Immunodeficiency 23
Purine nucleoside phosphorylase deficiency
Immunodeficiency 25
Autosomal dominant combined immunodeficiency
Immunodeficiency 101, varicella zoster virus-specific
Immunodeficiency 65, susceptibility to viral infections
Immunodeficiency 80 with or without congenital cardiomyopathy
Immunodeficiency 81
Immunodeficiency 91 and hyperinflammation
Non-severe combined immunodeficiency
Short stature, microcephaly, and endocrine dysfunction
Member diseases (most connected first ‐ the cluster's core)
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LIG4 | 9 / 24 | Acute lymphoblastic leukemia, Combined immunodeficiency, Dna ligase iv deficiency, Dubowitz syndrome and 5 more |
| CD247 | 4 / 24 | Immunodeficiency, Immunodeficiency 25, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| CD3E | 4 / 24 | Immunodeficiency, Immunodeficiency 18, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| CD3G | 4 / 24 | Combined immunodeficiency, Immunodeficiency, Immunodeficiency 17, cd3 gamma deficient, Severe combined immunodeficiency |
| CORO1A | 4 / 24 | Combined immunodeficiency, Immunodeficiency, Omenn syndrome, Severe combined immunodeficiency |
| DCLRE1C | 4 / 24 | Omenn syndrome, Severe combined immunodeficiency, Severe combined immunodeficiency autosomal recessive t-cell-negative/b-cell-negative/nk-cell-positive with sensitivity to ionizing radiation, T-b+ severe combined immunodeficiency |
| IL7R | 4 / 24 | Immunodeficiency, Omenn syndrome, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| PGM3 | 4 / 24 | Combined immunodeficiency, Immunodeficiency, Immunodeficiency 23, Severe combined immunodeficiency |
| PNP | 4 / 24 | Combined immunodeficiency, Purine nucleoside phosphorylase deficiency, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| PTPRC | 4 / 24 | Immunodeficiency, Omenn syndrome, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| RAG1 | 4 / 24 | Combined immunodeficiency, Omenn syndrome, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| RAG2 | 4 / 24 | Immunodeficiency, Omenn syndrome, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| BCL11B | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| CARD11 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| CARMIL2 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| CD3D | 3 / 24 | Immunodeficiency, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| CTPS1 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| FOXN1 | 3 / 24 | Combined immunodeficiency, Severe combined immunodeficiency, T-b+ severe combined immunodeficiency |
| IKBKB | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| IL21R | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Omenn syndrome |
| IL2RG | 3 / 24 | Combined immunodeficiency, Omenn syndrome, Severe combined immunodeficiency |
| JAK3 | 3 / 24 | Omenn syndrome, Severe combined immunodeficiency, T-B+ severe combined immunodeficiency |
| LCK | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| MALT1 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| ORAI1 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, T-b+ severe combined immunodeficiency |
| PRKDC | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| STIM1 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, T-b+ severe combined immunodeficiency |
| STK4 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| TFRC | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| ZAP70 | 3 / 24 | Combined immunodeficiency, Immunodeficiency, Severe combined immunodeficiency |
| ADA | 2 / 24 | Omenn syndrome, Severe combined immunodeficiency |
| ARPC1B | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| BLM | 2 / 24 | Acute lymphoblastic leukemia, Immunodeficiency |
| CD70 | 2 / 24 | Combined immunodeficiency, Severe combined immunodeficiency |
| CHD7 | 2 / 24 | Immunodeficiency, Omenn syndrome |
| COPG1 | 2 / 24 | Immunodeficiency, Non-severe combined immunodeficiency |
| DEF6 | 2 / 24 | Immunodeficiency, Immunodeficiency 87 and autoimmunity |
| DOCK2 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| DOCK8 | 2 / 24 | Combined immunodeficiency, Severe combined immunodeficiency |
| DOP1A | 2 / 24 | Immunodeficiency, Severe combined immunodeficiency |
| ERBIN | 2 / 24 | Autosomal dominant combined immunodeficiency, Combined immunodeficiency |
| FCHO1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| GINS1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| ICOSLG | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| IFTAP | 2 / 24 | Omenn syndrome, Severe combined immunodeficiency |
| IL2RA | 2 / 24 | Immunodeficiency, Omenn syndrome |
| IL6ST | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| IRF4 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| IRF9 | 2 / 24 | Immunodeficiency, Immunodeficiency 65, susceptibility to viral infections |
| LAT | 2 / 24 | Immunodeficiency, Severe combined immunodeficiency |
| LCP2 | 2 / 24 | Immunodeficiency, Immunodeficiency 81 |
| LRBA | 2 / 24 | Combined immunodeficiency, Severe combined immunodeficiency |
| MCM10 | 2 / 24 | Immunodeficiency, Immunodeficiency 80 with or without congenital cardiomyopathy |
| MSN | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| MST1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| NHEJ1 | 2 / 24 | Immunodeficiency, Severe combined immunodeficiency |
| NUDCD3 | 2 / 24 | Omenn syndrome, Severe combined immunodeficiency |
| PIK3CD | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| PIK3R1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| POLD1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| POLD3 | 2 / 24 | Immunodeficiency, Severe combined immunodeficiency |
| POLR3F | 2 / 24 | Immunodeficiency, Immunodeficiency 101, varicella zoster virus-specific |
| PSMB10 | 2 / 24 | Immunodeficiency, Omenn syndrome |
| RAC2 | 2 / 24 | Immunodeficiency, T-b+ severe combined immunodeficiency |
| REL | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| RELB | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| RFX5 | 2 / 24 | Combined immunodeficiency, Severe combined immunodeficiency |
| RHOH | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| SLC19A1 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| STAT5B | 2 / 24 | Combined immunodeficiency, T-b+ severe combined immunodeficiency |
| TBX1 | 2 / 24 | Combined immunodeficiency, T-b+ severe combined immunodeficiency |
| TNFRSF4 | 2 / 24 | Combined immunodeficiency, Immunodeficiency |
| TTC7A | 2 / 24 | Combined immunodeficiency, Severe combined immunodeficiency |
| XRCC4 | 2 / 24 | Lig4 syndrome, Short stature, microcephaly, and endocrine dysfunction |
| ZNFX1 | 2 / 24 | Immunodeficiency, Immunodeficiency 91 and hyperinflammation |
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 ⇵ |
|---|---|---|---|---|---|
| Primary immunodeficiency | KEGG | 20 / 38 | 32.1× | 1.94e-26 | 4.00e-23 ✓ sig. |
| Th17 cell differentiation | KEGG | 28 / 109 | 15.7× | 3.85e-26 | 7.46e-23 ✓ sig. |
| Measles | KEGG | 30 / 139 | 13.2× | 1.61e-25 | 2.86e-22 ✓ sig. |
| T cell receptor signaling pathway | KEGG | 28 / 122 | 14.0× | 1.17e-24 | 1.85e-21 ✓ sig. |
| Th1 and Th2 cell differentiation | KEGG | 24 / 93 | 15.7× | 1.42e-22 | 1.70e-19 ✓ sig. |
| Herpes simplex virus 1 infection | KEGG | 29 / 182 | 9.7× | 9.25e-21 | 7.89e-18 ✓ sig. |
| Epstein-Barr virus infection | KEGG | 30 / 204 | 9.0× | 2.05e-20 | 1.61e-17 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 20 / 90 | 13.5× | 1.41e-17 | 7.11e-15 ✓ sig. |
| Toll-like receptor signaling pathway | KEGG | 21 / 109 | 11.7× | 4.82e-17 | 2.17e-14 ✓ sig. |
| Influenza A | KEGG | 25 / 173 | 8.8× | 5.83e-17 | 2.58e-14 ✓ sig. |
| Osteoclast differentiation | KEGG | 23 / 142 | 9.9× | 8.27e-17 | 3.51e-14 ✓ sig. |
| JAK-STAT signaling pathway | KEGG | 23 / 168 | 8.3× | 3.72e-15 | 1.16e-12 ✓ sig. |
| NF-kappa B signaling pathway | KEGG | 19 / 105 | 11.0× | 5.41e-15 | 1.62e-12 ✓ sig. |
| NOD-like receptor signaling pathway | KEGG | 23 / 187 | 7.5× | 3.95e-14 | 1.01e-11 ✓ sig. |
| Chagas disease | KEGG | 18 / 103 | 10.7× | 5.49e-14 | 1.37e-11 ✓ 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 system process | GO:0002376 | 57 / 943 | 5.7× | 5.03e-28 | 2.34e-24 ✓ sig. |
| T cell activation | GO:0042110 | 22 / 76 | 27.5× | 4.27e-26 | 1.56e-22 ✓ sig. |
| T cell receptor signaling pathway | GO:0050852 | 24 / 121 | 18.8× | 4.76e-24 | 1.28e-20 ✓ sig. |
| T cell proliferation | GO:0042098 | 15 / 51 | 27.9× | 2.94e-18 | 3.63e-15 ✓ sig. |
| defense response to virus | GO:0051607 | 25 / 247 | 9.6× | 1.28e-17 | 1.48e-14 ✓ sig. |
| B cell differentiation | GO:0030183 | 16 / 80 | 19.0× | 1.88e-16 | 1.73e-13 ✓ sig. |
| positive regulation of T cell proliferation | GO:0042102 | 15 / 67 | 21.2× | 2.76e-16 | 2.46e-13 ✓ sig. |
| T cell differentiation | GO:0030217 | 14 / 54 | 24.6× | 2.95e-16 | 2.62e-13 ✓ sig. |
| response to virus | GO:0009615 | 18 / 128 | 13.3× | 1.63e-15 | 1.30e-12 ✓ sig. |
| cell surface receptor signaling pathway | GO:0007166 | 27 / 373 | 6.9× | 2.89e-15 | 2.16e-12 ✓ sig. |
| positive regulation of canonical NF-kappaB signal transduction | GO:0043123 | 22 / 232 | 9.0× | 5.01e-15 | 3.64e-12 ✓ sig. |
| innate immune response | GO:0045087 | 33 / 605 | 5.2× | 7.12e-15 | 4.98e-12 ✓ sig. |
| immune response | GO:0006955 | 31 / 543 | 5.4× | 1.50e-14 | 9.98e-12 ✓ sig. |
| cytokine-mediated signaling pathway | GO:0019221 | 18 / 145 | 11.8× | 1.53e-14 | 1.01e-11 ✓ sig. |
| positive regulation of tumor necrosis factor production | GO:0032760 | 16 / 113 | 13.4× | 5.70e-14 | 3.45e-11 ✓ sig. |