Table 1.
Twenty-three Treg transcriptomic datasets collected from the NIH-NCBI-GEO and EMBL-EBI databases were analyzed.
| Access ID | Group | Tissue | Comparison | PMID |
|---|---|---|---|---|
| GSE37532 | normal lymph node | lymph node | CD3+CD4+CD25+ Treg cells vs. CD3+CD4+CD25- Tconv | 25550516 |
| E-MTAB-7961 | normal spleen | Spleen | CD45+ CD4+ TCRB+ Foxp3+ Treg vs CD45+ CD4+ TCRB+ Foxp3- Tconv | 32051345 |
| GSE64909 | normal tissue | Brown adipose tissue(BAT) | CD4+CD25+Foxp3+ Treg vs CD4+Foxp3- Tconv | 25714366 |
| E-MTAB-7961 | normal tissue | Kidney | CD45+ CD4+ TCRB+ Foxp3+ Treg vs CD45+ CD4+ TCRB+ Foxp3- Tconv | 32051345 |
| GSE50096 | benign disease spleen | Skeletal muscle injured 2w spleen |
CD4+ Foxp3+ Treg vs CD4+ Foxp3- Tconv | 24315098 |
| GSE50096 | benign disease spleen | Skeletal muscle injured 4d spleen |
CD4+ Foxp3+ Treg vs CD4+ Foxp3- Tconv | 24315098 |
| E-MTAB-7961 | benign disease tissue | Kidney Fibrosis | CD45+ CD4+ TCRB+ Foxp3+ Treg vs CD45+ CD4+ TCRB+ Foxp3- Tconv | 32051345 |
| E-MTAB-7961 | benign disease tissue | Kidney Regeneration | CD45+ CD4+ TCRB+ Foxp3+ Treg vs CD45+ CD4+ TCRB+ Foxp3- Tconv | 32051345 |
| GSE50096 | benign disease tissue | Skeletal muscle injured 2w muscle | CD4+ Foxp3+ Treg vs CD4+ Foxp3- Tconv | 24315098 |
| GSE50096 | benign disease tissue | Skeletal muscle injured 4d muscle | CD4+ Foxp3+ Treg vs CD4+ Foxp3- Tconv | 24315098 |
| GSE116347 | tumor spleen | Tumor Bearing Mouse (B16) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
| GSE116347 | tumor spleen | Tumor Bearing Mouse (MC38) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
| GSE116347 | tumor spleen | mTumor Bearing Mouse (CT26) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
| GSE120280 | tumor spleen | Lung Tumor(TC-1) Bearing Mouse | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | NA |
| GSE103523* | tumor tissue | Hepatocellular carcinoma | CD14-CD4+CD25high Treg cells vs. CD3+CD4+CD25- Tconv cells | 29941600 |
| GSE139372 | tumor tissue | Melanoma | CD4+CD8- CD25+CD27+ Treg vs CD4+CD8- CD25-CD27- Teff | 31852848 |
| GSE120280 | tumor tissue | Lung Tumor(TC-1) Bearing Mouse | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | NA |
| GSE89225 | tumor tissue | Breast Cancer | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 27851913 |
| GSE116347 | tumor tissue | Tumor Bearing Mouse (B16) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
| GSE116347 | tumor tissue | Tumor Bearing Mouse (MC38) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
| GSE116347 | tumor tissue | Tumor Bearing Mouse (CT26) | CD4+Foxp3+ Treg vs CD4+Foxp3- Tconv | 30348759 |
NIH-NIBI-GEO, National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)- Gene Expression Omnibus (GEO) databases https://www.ncbi.nlm.nih.gov/gds/; EMBL-EBI, European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute(EBI) https://www.ebi.ac.uk/arrayexpress/; Mouse models involved in this study were described in supplementary table 2. Access ID start with “GSE” was a dataset from GEO database, whereas start with “E-MTAB” was a dataset from EMBL-EBI dataset. GFP, green fluorescence protein; TCRB, T cell receptor beta locus. NA, Not Available.
*Up to August 14th, 2020, a total of 7 datasets of Treg vs Tconv in malignant tumor tissue were found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE103523 was excluded because Foxp3 was not a significantly DEG in this dataset.
The differentially expressed genes (DEGs) of Treg versus (vs) CD4+Foxp3- T effector cells were screened as a p < 0.05 and absolute |log2FC|>= 1. The datasets were grouped as normal, benign disease and malignant Lymphoid and non-lymphoid tissues.