Adaptive Immunity: Coverage Tables
Generated by projects/ADAPTIVE_IMMUNITY/scripts/coverage.py from
areas.yaml, genes/human/*/*-ai-review.yaml, modules/*.yaml and
gocams/index.tsv. Do not edit by hand; re-run the script.
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Summary by area
| Area | Anchor genes | Reviewed | COMPLETE | In a human GO-CAM | Modules |
|---|---|---|---|---|---|
| MHC class I antigen processing and presentation | 8 | 0 | 0 | 6 | none |
| MHC class II antigen processing and presentation | 7 | 0 | 0 | 0 | none |
| V(D)J recombination | 7 | 0 | 0 | 1 | none |
| T cell receptor signaling | 19 | 19 | 19 | 10 | t_cell_receptor_signaling |
| T cell co-stimulation and inhibitory checkpoints | 9 | 3 | 2 | 8 | none |
| IL-2 and common gamma-chain cytokine signaling | 11 | 5 | 3 | 10 | jak_stat_signaling |
| Helper and regulatory T cell differentiation | 9 | 5 | 2 | 4 | none |
| T cell mediated cytotoxicity | 7 | 0 | 0 | 4 | none |
| B cell receptor signaling | 12 | 5 | 4 | 6 | b_cell_receptor_signaling |
| B cell differentiation and germinal center | 10 | 1 | 0 | 3 | none |
| Class switch recombination and somatic hypermutation | 6 | 1 | 0 | 2 | none |
| Antibody transport and Fc receptor effector signaling | 7 | 0 | 0 | 1 | fc_gamma_receptor_signaling, fc_epsilon_receptor_signaling |
| Unique genes | 110 | 38 | 30 | 55 |
Module grounding
UniProtKB accessions grounded in each module and how many have a human review.
| Module | Status | Grounded proteins | With review |
|---|---|---|---|
t_cell_receptor_signaling |
DRAFT | 19 | 19 |
jak_stat_signaling |
DRAFT | 10 | 8 |
b_cell_receptor_signaling |
DRAFT | 7 | 3 |
fc_gamma_receptor_signaling |
DRAFT | 7 | 2 |
fc_epsilon_receptor_signaling |
DRAFT | 7 | 2 |
Anchor genes by area
MHC class I antigen processing and presentation
Grounding terms: GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
HLA-A |
no review | 1 |
HLA-B |
no review | 0 |
B2M |
no review | 1 |
TAP1 |
no review | 4 |
TAP2 |
no review | 4 |
TAPBP |
no review | 4 |
ERAP1 |
no review | 1 |
ERAP2 |
no review | 0 |
MHC class II antigen processing and presentation
Grounding terms: GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
HLA-DRA |
no review | 0 |
HLA-DRB1 |
no review | 0 |
HLA-DMA |
no review | 0 |
HLA-DMB |
no review | 0 |
CD74 |
no review | 0 |
CTSS |
no review | 0 |
CIITA |
no review | 0 |
V(D)J recombination
Grounding terms: GO:0033151 V(D)J recombination.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
RAG1 |
no review | 0 |
RAG2 |
no review | 0 |
DCLRE1C |
no review | 0 |
PRKDC |
no review | 3 |
LIG4 |
no review | 0 |
NHEJ1 |
no review | 0 |
DNTT |
no review | 0 |
T cell receptor signaling
Grounding terms: GO:0050852 T cell receptor signaling pathway.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
| human/CD3D | COMPLETE | 0 |
| human/CD3E | COMPLETE | 8 |
| human/CD3G | COMPLETE | 0 |
| human/CD247 | COMPLETE | 6 |
| human/CD4 | COMPLETE | 12 |
| human/CD8A | COMPLETE | 0 |
| human/CD8B | COMPLETE | 0 |
| human/LCK | COMPLETE | 15 |
| human/PTPRC | COMPLETE | 1 |
| human/ZAP70 | COMPLETE | 12 |
| human/LAT | COMPLETE | 3 |
| human/LCP2 | COMPLETE | 0 |
| human/GRAP2 | COMPLETE | 0 |
| human/ITK | COMPLETE | 0 |
| human/PLCG1 | COMPLETE | 0 |
| human/PPP3CA | COMPLETE | 1 |
| human/PPP3CB | COMPLETE | 1 |
| human/PPP3R1 | COMPLETE | 0 |
| human/NFATC1 | COMPLETE | 1 |
T cell co-stimulation and inhibitory checkpoints
Grounding terms: GO:0031295 T cell costimulation.
Related projects: AUTOIMMUNE.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
| human/CD28 | COMPLETE | 6 |
CD80 |
no review | 4 |
CD86 |
no review | 4 |
ICOS |
no review | 1 |
| human/CTLA4 | COMPLETE | 2 |
PDCD1 |
no review | 5 |
CD274 |
no review | 3 |
LAG3 |
no review | 4 |
| human/PTPN22 | IN_PROGRESS | 0 |
IL-2 and common gamma-chain cytokine signaling
Grounding terms: GO:0038110 interleukin-2-mediated signaling pathway.
Related projects: AUTOIMMUNE.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
IL2 |
no review | 3 |
| human/IL2RA | DRAFT | 1 |
IL2RB |
no review | 2 |
IL2RG |
no review | 6 |
IL7 |
no review | 2 |
| human/IL7R | IN_PROGRESS | 3 |
IL21R |
no review | 0 |
| human/JAK1 | COMPLETE | 22 |
JAK3 |
no review | 6 |
| human/STAT5A | COMPLETE | 10 |
| human/STAT5B | COMPLETE | 4 |
Helper and regulatory T cell differentiation
Grounding terms: GO:0046632 alpha-beta T cell differentiation.
Related projects: AUTOIMMUNE.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
TBX21 |
no review | 0 |
| human/GATA3 | COMPLETE | 0 |
RORC |
no review | 1 |
FOXP3 |
no review | 2 |
BCL6 |
no review | 0 |
| human/STAT4 | DRAFT | 2 |
| human/STAT3 | COMPLETE | 27 |
| human/IRF4 | DRAFT | 0 |
| human/BACH2 | DRAFT | 0 |
T cell mediated cytotoxicity
Grounding terms: GO:0001913 T cell mediated cytotoxicity.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
PRF1 |
no review | 5 |
GZMA |
no review | 2 |
GZMB |
no review | 3 |
FASLG |
no review | 1 |
UNC13D |
no review | 0 |
STX11 |
no review | 0 |
STXBP2 |
no review | 0 |
B cell receptor signaling
Grounding terms: GO:0050853 B cell receptor signaling pathway.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
CD79A |
no review | 0 |
CD79B |
no review | 0 |
CD19 |
no review | 1 |
CR2 |
no review | 3 |
| human/LYN | COMPLETE | 7 |
SYK |
no review | 14 |
| human/BTK | DRAFT | 2 |
| human/BLNK | COMPLETE | 0 |
| human/PLCG2 | COMPLETE | 1 |
| human/PIK3CD | COMPLETE | 0 |
CD22 |
no review | 0 |
FCGR2B |
no review | 0 |
B cell differentiation and germinal center
Grounding terms: GO:0030183 B cell differentiation; GO:0002467 germinal center formation.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
PAX5 |
no review | 0 |
EBF1 |
no review | 0 |
CD40 |
no review | 2 |
CD40LG |
no review | 2 |
CXCR5 |
no review | 0 |
CXCL13 |
no review | 0 |
SH2D1A |
no review | 1 |
BCL6 |
no review | 0 |
PRDM1 |
no review | 0 |
| human/IRF4 | DRAFT | 0 |
Class switch recombination and somatic hypermutation
Grounding terms: GO:0045190 isotype switching; GO:0016446 somatic hypermutation of immunoglobulin genes.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
| human/AICDA | DRAFT | 0 |
UNG |
no review | 1 |
MSH2 |
no review | 0 |
MSH6 |
no review | 0 |
POLH |
no review | 0 |
REV1 |
no review | 1 |
Antibody transport and Fc receptor effector signaling
Grounding terms: GO:0006959 humoral immune response.
| Gene | Review status | Human GO-CAM models |
|---|---|---|
FCGRT |
no review | 0 |
PIGR |
no review | 0 |
FCGR1A |
no review | 0 |
FCGR2A |
no review | 0 |
FCGR3A |
no review | 1 |
FCER1A |
no review | 0 |
FCER1G |
no review | 0 |