Table 1.
Key resource table.
| Resource | Source | Identifier |
|---|---|---|
| Deposited Data | ||
| Solid tumor samples | CCLE | https://portals.broadinstitute.org/ |
| Immune cell from healthy individuals | DICE | https://dice-database.org/ |
| Pan-cancer tumor samples (21 types) | TCGA | http://firebrowse.org/ |
| Sorted PD-1hi/low/negCD8+ T cells from NSCLC | Thommen et al. (13) | SRA: SRP108393 |
| Sorted PD-1hi/low/negCD8+ T cells from HCC, flow cytometry, and RNA-seq results | Kim et al. (14) | GEO: GSE111389 |
| Sorted PD-1hi/low/negCD8+ T cells from breast cancer | Guo et al. (15) | SRA: SRP189910 |
| Anti-PD-1/anti-PD-1 combined with anti-CTLA4 treated melanoma (Gide) | Gide et al. (16) | ENA: ERP105482 |
| Anti-PD-1 treated melanoma (Riaz) | Riaz et al. (17) | SRA: SRP094781 |
| Anti-PD-1 treated gastric cancer | Kim et al. (18) | ENA: ERP107734 |
| Anti-PD-L1 treated urothelial cancer | Mariathasan et al. (5) | http://research-pub.gene.com/IMvigor210CoreBiologies/ |
| Anti-PD-1/PD-L1 treated NSCLC (Jung) | Jung et al. (19) | GEO: GSE135222 |
| Anti-PD-1 treated NSCLC (Cho) | Cho et al. (20) | GEO: GSE126044 |
| ScRNA-seq of immune cells in melanoma TME | Sade-Feldman et al. (21) | GEO: GSE120575 |
| ScRNA-seq of T cells in NSCLC TME | Guo et al. (22) | GEO: GSE99254 |
| Anti-PD1/anti-CTLA4 combination therapy treated mouse model of breast cancer | Hollern et al. (23) | GEO: GSE124821 |
| Human genome (GRCH38/hg38) | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human |
| Software and Algorithms | ||
| STAR version 2.5.4b | Dobin et al. (24) | https://github.com/alexdobin/STAR |
| Stringtie, version v1.3.4d | Pertea et al. (25) | https://ccb.jhu.edu/software/stringtie/ |
| Metascape | Zhou et al. (26) | https://metascape.org/ |
| CellPhoneDB | Efremova et al. (27) | https://github.com/Teichlab/cellphonedb |
| MSigDB | – | http://www.gsea-msigdb.org/gsea/msigdb |
| CIBERSORT | Newman et al. (28) | https://cibersort.stanford.edu/ |
| quanTIseq | Finotello et al. (29) | https://github.com/icbi-lab/quanTIseq |
| R packages/scripts | ||
| Codes used for scoring | This paper | https://github.com/Liulab/PD1highCD8Tscore |
| DESeq2 (1.26.0) | Love et al. (30) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| limma (3.41.16) | Ritchie et al. (31) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| singscore (1.10.0) | Foroutan et al. (32) | https://www.bioconductor.org/packages/release/bioc/html/singscore.html |
| Seurat (3.1.0) | Butler et al. (33) | https://satijalab.org/seurat/ |
| edgeR (3.27.13) | Robinson et al. (34) | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| fgsea (1.12.0) | Sergushichev (35) | http://bioconductor.org/packages/release/bioc/html/fgsea.html |
| pROC (1.15.3) | Robin et al. (36) | https://cran.r-project.org/web/packages/pROC/index.html |
| survival (3.1-12) | – | https://cran.r-project.org/web/packages/survival/index.html |
| survminer (0.4.8) | – | https://cran.r-project.org/web/packages/survminer/index.html |
| biomaRt (2.42.0) | Durinck et al. (37) | https://bioconductor.org/packages/release/bioc/html/biomaRt.html |
| immunophenoscore | Charoentong et al. (38) | https://tcia.at/tools/toolsMain |