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# **References**
If IOBR R package is utilized in your published research, please cite:
Zeng D, Ye Z, Shen R, Yu G, Wu J, Xiong Y,..., Liao W (2021) **IOBR**: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. *Frontiers in Immunology*. 12:687975. [doi: 10.3389/fimmu.2021.687975](https://www.frontiersin.org/articles/10.3389/fimmu.2021.687975/full)
## TME deconvolution
Please cite the following papers appropriately for TME deconvolution algorithm if used:
**CIBERSORT**: Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., … Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods, 12(5), 453–457. https://doi.org/10.1038/nmeth.3337
**ESTIMATE**: Vegesna R, Kim H, Torres-Garcia W, ..., Verhaak R.*(2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature Communications 4, 2612. http://doi.org/10.1038/ncomms3612
**quanTIseq**: Finotello, F., Mayer, C., Plattner, C., Laschober, G., Rieder, D., Hackl, H., ..., Sopper, S.* (2019). Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome medicine, 11(1), 34. https://doi.org/10.1186/s13073-019-0638-6
**TIMER**: Li, B., Severson, E., Pignon, J.-C., Zhao, H., Li, T., Novak, J., … Liu, X. S.* (2016). Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biology, 17(1), 174.
**IPS**: P. Charoentong et al.*, Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Reports 18, 248-262 (2017). https://doi.org/10.1016/j.celrep.2016.12.019
**MCPCounter**: Becht, E., Giraldo, N. A., Lacroix, L., Buttard, B., Elarouci, N., Petitprez, F., … de Reyniès, A*. (2016). Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biology, 17(1), 218. https://doi.org/10.1186/s13059-016-1070-5
**xCell**: Aran, D., Hu, Z., & Butte, A. J.* (2017). xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biology, 18(1), 220. https://doi.org/10.1186/s13059-017-1349-1
**EPIC**: Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D*. (2017). Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. ELife, 6, e26476. https://doi.org/10.7554/eLife.26476
## TME Signatures
For signature score estimation, please cite corresponding literature below:
**ssgsea**: Barbie, D.A. et al (2009). Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature, 462(5):108-112.
**gsva**: Hänzelmann, S., Castelo, R. and Guinney, J. (2013). GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14(1):7.
**zscore**: Lee, E. et al (2008). Inferring pathway activity toward precise disease classification. PLoS Comp Biol, 4(11):e1000217.
## Data sets
For the datasets enrolled in IOBR, please cite the data sources:
**UCSCXena**: Wang et al.,et al (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Journal of Open Source Software, 4(40), 1627
**TLSscore**: Helmink BA, Reddy SM, Gao J, et al. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020 Jan;577(7791):549-555.
**IMvigor210 immuntherapy cohort**: Mariathasan S, Turley SJ, Nickles D, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018 Feb 22;554(7693):544-548.
**HCP5**: Kulski, J.K. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019, 8, 480.
**HCP5**: Li, Y., Jiang, T., Zhou, W. et al. Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers. Nat Commun 11, 1000 (2020).
HCP5: Sun J, Zhang Z, Bao S, et alIdentification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancerJournal for ImmunoTherapy of Cancer 2020;8:e000110.
**LINC00657**: Feng Q, Zhang H, Yao D, Chen WD, Wang YD. Emerging Role of Non-Coding RNAs in Esophageal Squamous Cell Carcinoma. Int J Mol Sci. 2019 Dec 30;21(1):258. doi: 10.3390/ijms21010258.
**LINC00657**: Qin X, Zhou M, Lv H, Mao X, Li X, Guo H, Li L, Xing H. Long noncoding RNA LINC00657 inhibits cervical cancer development by sponging miR-20a-5p and targeting RUNX3. Cancer Lett. 2020 Oct 28:S0304-3835(20)30578-4. doi: 10.1016/j.canlet.2020.10.044.
**LINC00657**: Zhang XM, Wang J, Liu ZL, Liu H, Cheng YF, Wang T. LINC00657/miR-26a-5p/CKS2 ceRNA network promotes the growth of esophageal cancer cells via the MDM2/p53/Bcl2/Bax pathway. Biosci Rep. 2020;40(6):BSR20200525.
**TCGA-STAD**: Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. doi: 10.1038/nature13480.
TCGA.STAD MAF data: https://api.gdc.cancer.gov/data/c06465a3-50e7-46f7-b2dd-7bd654ca206b
## Others
1. Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., … Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods, 12(5), 453–457.
2. Vegesna R, Kim H, Torres-Garcia W, ..., Verhaak R.*(2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature Communications 4, 2612.
3. Rieder, D., Hackl, H., ..., Sopper, S.* (2019). Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome medicine, 11(1), 34.
4. Li, B., Severson, E., Pignon, J.-C., Zhao, H., Li, T., Novak, J., … Liu, X. S.* (2016). Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biology, 17(1), 174.
5. P. Charoentong et al.*, Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Reports 18, 248-262 (2017).
6. Becht, E., Giraldo, N. A., Lacroix, L., Buttard, B., Elarouci, N., Petitprez, F., … de Reyniès, A*. (2016). Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biology, 17(1), 218.
7. Aran, D., Hu, Z., & Butte, A. J.* (2017). xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biology, 18(1), 220.
8. Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D*. (2017). Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. ELife, 6, e26476.
9. Barbie, D.A. et al (2009). Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature, 462(5):108-112.
10. Hänzelmann, S., Castelo, R. and Guinney, J. (2013). GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14(1):7.
11. Lee, E. et al (2008). Inferring pathway activity toward precise disease classification. PLoS Comp Biol, 4(11):e1000217.
12. Wang et al.,et al (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Journal of Open Source Software, 4(40), 1627
13. Helmink BA, Reddy SM, Gao J, et al. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020 Jan;577(7791):549-555.
14. Mariathasan S, Turley SJ, Nickles D, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018 Feb 22;554(7693):544-548.
15. Kulski, J.K. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019, 8, 480.
16. Li, Y., Jiang, T., Zhou, W. et al. Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers. Nat Commun 11, 1000 (2020).
17. Sun J, Zhang Z, Bao S, et alIdentification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancerJournal for ImmunoTherapy of Cancer 2020;8:e000110.
18. Feng Q, Zhang H, Yao D, Chen WD, Wang YD. Emerging Role of Non-Coding RNAs in Esophageal Squamous Cell Carcinoma. Int J Mol Sci. 2019 Dec 30;21(1):258. doi: 10.3390/ijms21010258.
19. Qin X, Zhou M, Lv H, Mao X, Li X, Guo H, Li L, Xing H. Long noncoding RNA LINC00657 inhibits cervical cancer development by sponging miR-20a-5p and targeting RUNX3. Cancer Lett. 2020 Oct
20. Zhang XM, Wang J, Liu ZL, Liu H, Cheng YF, Wang T. LINC00657/miR-26a-5p/CKS2 ceRNA network promotes the growth of esophageal cancer cells via the MDM2/p53/Bcl2/Bax pathway. Biosci Rep. 2020;40(6):BSR20200525.
21. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. doi: 10.1038/nature13480.