1. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a cancer journal for clinicians. 2018;68(6):394-424.
2. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature. 2000;406(6797):747-52.
3. Prat A, Perou CM. Deconstructing the molecular portraits of breast cancer. Molecular oncology. 2011;5(1):5-23.
4. Goldhirsch A, Wood WC, Coates AS, Gelber RD, Thurlimann B, Senn HJ. Strategies for subtypes--dealing with the diversity of breast cancer: highlights of the St. Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011. Annals of oncology : official journal of the European Society for Medical Oncology. 2011;22(8):1736-47.
5. Blows FM, Driver KE, Schmidt MK, Broeks A, van Leeuwen FE, Wesseling J, et al. Subtyping of breast cancer by immunohistochemistry to investigate a relationship between subtype and short and long term survival: a collaborative analysis of data for 10,159 cases from 12 studies. PLoS medicine. 2010;7(5):e1000279.
6. Kim J, Bae JS. Tumor-Associated Macrophages and Neutrophils in Tumor Microenvironment. Mediators Inflamm. 2016;2016:6058147.
7. Zeng D, Zhou R, Yu Y, Luo Y, Zhang J, Sun H, et al. Gene expression profiles for a prognostic immunoscore in gastric cancer. Br J Surg. 2018;105(10):1338-48.
8. Jiang Y, Zhang Q, Hu Y, Li T, Yu J, Zhao L, et al. ImmunoScore Signature: A Prognostic and Predictive Tool in Gastric Cancer. Ann Surg. 2018;267(3):504-13.
9. Mantovani A, Marchesi F, Malesci A, Laghi L, Allavena P. Tumour-associated macrophages as treatment targets in oncology. Nat Rev Clin Oncol. 2017;14(7):399-416.
10. Kalluri R. The biology and function of fibroblasts in cancer. Nat Rev Cancer. 2016;16(9):582-98.
11. Fridman WH, Zitvogel L, Sautes-Fridman C, Kroemer G. The immune contexture in cancer prognosis and treatment. Nat Rev Clin Oncol. 2017;14(12):717-34.
12. Turley SJ, Cremasco V, Astarita JL. Immunological hallmarks of stromal cells in the tumour microenvironment. Nat Rev Immunol. 2015;15(11):669-82.
13. Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet. 2016;387(10031):1909-20.
14. Nishino M, Ramaiya NH, Hatabu H, Hodi FS. Monitoring immune-checkpoint blockade: response evaluation and biomarker development. Nat Rev Clin Oncol. 2017;14(11):655-68.
15. Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, et al. TGFbeta attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554(7693):544-8.
16. Lee K, Hwang H, Nam KT. Immune response and the tumor microenvironment: how they communicate to regulate gastric cancer. Gut Liver. 2014;8(2):131-9.
17. Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453-7.
18. Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17(1):218.
19. Yoshihara K, Shahmoradgoli M, Martinez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
20. Fu H, Zhu Y, Wang Y, Liu Z, Zhang J, Xie H, et al. Identification and Validation of Stromal Immunotype Predict Survival and Benefit from Adjuvant Chemotherapy in Patients with Muscle-Invasive Bladder Cancer. Clin Cancer Res. 2018;24(13):3069-78.
21. Zeng D, Li M, Zhou R, Zhang J, Sun H, Shi M, et al. Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures. Cancer Immunol Res. 2019;7(5):737-50.
22. Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, Farooqi HK, et al. Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics. 2008;1:52.
23. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001;98(19):10869-74.
24. Zhang S, Wang Y, Gu Y, Zhu J, Ci C, Guo Z, et al. Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns. Mol Oncol. 2018;12(7):1047-60.
25. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
26. Mirzal A. Nonparametric Tikhonov Regularized NMF and Its Application in Cancer Clustering. IEEE/ACM Trans Comput Biol Bioinform. 2014;11(6):1208-17.
27. Yu N, Gao YL, Liu JX, Shang J, Zhu R, Dai LY. Co-differential Gene Selection and Clustering Based on Graph Regularized Multi-View NMF in Cancer Genomic Data. Genes (Basel). 2018;9(12).
28. Ye C, Toyoda K, Ohtsuki T. Blind Source Separation on Non-contact Heartbeat Detection by Non-negative Matrix Factorization Algorithms. IEEE Trans Biomed Eng. 2019.
29. Boillaud E, Molina G. Are judgments a form of data clustering? Reexamining contrast effects with the k-means algorithm. J Exp Psychol Hum Percept Perform. 2015;41(2):415-30.
30. Shi W, Zou R, Yang M, Mai L, Ren J, Wen J, et al. Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks. Frontiers in physiology. 2019;10:662.
31. Huffaker TB, Lee SH, Tang WW, Wallace JA, Alexander M, Runtsch MC, et al. Antitumor immunity is defective in T cell-specific microRNA-155-deficient mice and is rescued by immune checkpoint blockade. The Journal of biological chemistry. 2017;292(45):18530-41.
32. Shao M, Wen ZB, Yang HH, Zhang CY, Xiong JB, Guan XX, et al. Exogenous angiotensin (1-7) directly inhibits epithelial-mesenchymal transformation induced by transforming growth factor-beta1 in alveolar epithelial cells. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie. 2019;117:109193.
33. Ghasemi A, Zahediasl S. Normality tests for statistical analysis: a guide for non-statisticians. Int J Endocrinol Metab. 2012;10(2):486-9.
34. Hazra A, Gogtay N. Biostatistics Series Module 3: Comparing Groups: Numerical Variables. Indian J Dermatol. 2016;61(3):251-60.
35. Luthra S, Chandran U, Diergaarde B, Becich M, Lee AV, Neumann CA. Expression of reactive species related genes is associated with patient survival in luminal B breast cancer. Free radical biology & medicine. 2018;120:170-80.
36. Li Z, Zhang Y, Zhang Z, Zhao Z, Lv Q. A four-gene signature predicts the efficacy of paclitaxel-based neoadjuvant therapy in human epidermal growth factor receptor 2-negative breast cancer. Journal of cellular biochemistry. 2019;120(4):6046-56.
37. Xie X, Wang J, Shi D, Zou Y, Xiong Z, Li X, et al. Identification of a 4-mRNA metastasis-related prognostic signature for patients with breast cancer. Journal of cellular and molecular medicine. 2019;23(2):1439-47.
38. Paget S. The distribution of secondary growths in cancer of the breast. 1889. Cancer metastasis reviews. 1989;8(2):98-101.
39. Junttila MR, de Sauvage FJ. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature. 2013;501(7467):346-54.
40. Miller JF, Sadelain M. The journey from discoveries in fundamental immunology to cancer immunotherapy. Cancer cell. 2015;27(4):439-49.
41. Sharma P, Hu-Lieskovan S, Wargo JA, Ribas A. Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy. Cell. 2017;168(4):707-23.
42. Sharpe AH, Pauken KE. The diverse functions of the PD1 inhibitory pathway. Nature reviews Immunology. 2018;18(3):153-67.
43. Cristescu R, Mogg R, Ayers M, Albright A, Murphy E, Yearley J, et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science. 2018;362(6411).
44. Sen T, Della Corte CM, Milutinovic S, Cardnell RJ, Diao L, Ramkumar K, et al. Combination treatment of the oral CHK1 inhibitor, SRA737 and low dose gemcitabine, enhances the effect of PD-L1 blockade by modulating the immune microenvironment in small cell lung cancer. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 2019.
45. Yu M, Duan X, Cai Y, Zhang F, Jiang S, Han S, et al. Multifunctional Nanoregulator Reshapes Immune Microenvironment and Enhances Immune Memory for Tumor Immunotherapy. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2019;6(16):1900037.
46. Moeini A, Torrecilla S, Tovar V, Montironi C, Andreu-Oller C, Peix J, et al. An Immune Gene Expression Signature Associated With Development of Human Hepatocellular Carcinoma Identifies Mice That Respond to Chemopreventive Agents. Gastroenterology. 2019.
47. Zemek RM, De Jong E, Chin WL, Schuster IS, Fear VS, Casey TH, et al. Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment. Science translational medicine. 2019;11(501).
48. Wang X, Su D, Qin Z, Chen Z. Identification of FOXN4 as a tumor suppressor of breast carcinogenesis via the activation of TP53 and deactivation of Notch signaling. Gene. 2019:144057.