Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Centers NHGRI, for Common Disease Genomics; Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020;583(7814):83–9. https://doi.org/10.1038/s41586-020-2371-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Allaire J, Xie Y, Dervieux C, McPherson J, Luraschi J, Ushey K, Atkins A, Wickham H, Cheng J, Chang W, Iannone R. _rmarkdown: Dynamic Documents for R_. R package version 2.21. 2023. https://github.com/rstudio/rmarkdown.

Allison KH, et al. Estrogen and progesterone receptor testing in breast cancer: ASCO/CAP guideline update. J Clin Oncol. 2020;38:1346–66.

Article  PubMed  Google Scholar 

Arora S. GSE62944: GEO accession data GSE62944 as a SummarizedExperiment. R package version 1.28.1. 2023. http://bioconductor.org/packages/release/bioc/html/GSE62944.html.

Bae SY, Kim S, Lee JH, Lee HC, Lee SK, Kil WH, Kim SW, Lee JE, Nam SJ. Poor prognosis of single hormone receptor-positive breast cancer: similar outcome as triple-negative breast cancer. BMC Cancer. 2015;18(15):138. https://doi.org/10.1186/s12885-015-1121-4.

Article  CAS  Google Scholar 

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R. A comprehensive pan-cancer molecular study of gynecologic and breast cancers. Cancer Cell. 2018;33(4):690-705.e9. https://doi.org/10.1016/j.ccell.2018.03.014.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berghoff AS, Hielscher T, Ricken G, Furtner J, Schrimpf D, Widhalm G, Rajky U, Marosi C, Hainfellner JA, von Deimling A, Sahm F, Preusser M. Prognostic impact of genetic alterations and methylation classes in meningioma. Brain Pathol. 2022;32(2): e12970. https://doi.org/10.1111/bpa.12970.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berkel C, Cacan E. Half of most frequently mutated genes in breast cancer are expressed differentially between premenopausal and postmenopausal breast cancer patients. Cancer Genet. 2024;286–287:11–7. https://doi.org/10.1016/j.cancergen.2024.06.001.

Article  CAS  PubMed  Google Scholar 

Berkel C, Cacan E. Lower expression of NINJ1 (Ninjurin 1), a mediator of plasma membrane rupture, is associated with advanced disease and worse prognosis in serous ovarian cancer. Immunol Res. 2023;71(1):15–28. https://doi.org/10.1007/s12026-022-09323-7.

Article  CAS  PubMed  Google Scholar 

Berkel C. Retrospective analysis of transcriptomic differences between triple-negative breast cancer (TNBC) and non-TNBC. European J Biol. 2024;83(1):19–27.

Google Scholar 

Bi L, Wang H, Tian Y. Silencing FAM135B enhances radiosensitivity of esophageal carcinoma cell. Gene. 2021;772:145358. https://doi.org/10.1016/j.gene.2020.145358.

Article  CAS  PubMed  Google Scholar 

Bodle CR, Mackie DI, Roman DL. RGS17: an emerging therapeutic target for lung and prostate cancers. Future Med Chem. 2013;5(9):995–1007. https://doi.org/10.4155/fmc.13.91.

Article  CAS  PubMed  Google Scholar 

Bodle CR, Schamp JH, O’Brien JB, Hayes MP, Wu M, Doorn JA, Roman DL. Screen Targeting Lung and Prostate Cancer Oncogene Identifies Novel Inhibitors of RGS17 and Problematic Chemical Substructures. SLAS Discov. 2018;4:363–74. https://doi.org/10.1177/2472555217752301.

Article  CAS  Google Scholar 

Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61–70. https://doi.org/10.1038/nature11412.

Article  CAS  Google Scholar 

Cancer Genome Atlas Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. the cancer genome atlas pan-cancer analysis project. Nat Genet. 2013;45(10):1113–20. https://doi.org/10.1038/ng.2764.

Article  CAS  Google Scholar 

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, TCGA Research Network, Perou CM. Comprehensive molecular portraits of invasive lobular breast cancer. Cell. 2015;163(2):506–19. https://doi.org/10.1016/j.cell.2015.09.033.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Conrad DF, Pinto D, Redon R, et al. Origins and functional impact of copy number variation in the human genome. Nature. 2010;464(7289):704–12. https://doi.org/10.1038/nature08516.

Article  CAS  PubMed  Google Scholar 

Dauphine C, Moazzez A, Neal JC, Chlebowski RT, Ozao-Choy J. Single hormone receptor-positive breast cancers have distinct characteristics and survival. Ann Surg Oncol. 2020;27:4687–94. https://doi.org/10.1245/s10434-020-08898-5.

Article  PubMed  Google Scholar 

Diep CH, Daniel AR, Mauro LJ, Knutson TP, Lange CA. Progesterone action in breast, uterine, and ovarian cancers. J Mol Endocrinol. 2015;54(2):R31-53. https://doi.org/10.1530/JME-14-0252.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong D, Zhang W, Xiao W, Wu Q, Cao Y, Gao X, Huang L, Wang Y, Chen J, Wang W, Zhan Q. A GRN autocrine-dependent FAM135B/AKT/mTOR feedforward loop promotes esophageal squamous cell carcinoma progression. Cancer Res. 2021;81(4):910–22. https://doi.org/10.1158/0008-5472.CAN-20-0912.

Article  CAS  PubMed  Google Scholar 

Falini B, Agostinelli C, Bigerna B, Pucciarini A, Pacini R, Tabarrini A, Falcinelli F, Piccioli M, Paulli M, Gambacorta M, Ponzoni M, Tiacci E, Ascani S, Martelli MP, Dalla Favera R, Stein H, Pileri SA. IRTA1 is selectively expressed in nodal and extranodal marginal zone lymphomas. Histopathology. 2012;61(5):930–41. https://doi.org/10.1111/j.1365-2559.2012.04289.x.

Article  PubMed  Google Scholar 

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. https://doi.org/10.1186/gb-2004-5-10-r80.

Article  PubMed  PubMed Central  Google Scholar 

Hester J, Bryan J. glue: Interpreted String Literals. R package version 1.6.2. 2022. https://CRAN.R-project.org/package=glue.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods. 2015;12(2):115–21. https://doi.org/10.1038/nmeth.3252.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ikeda JI, Kohara M, Tsuruta Y, Nojima S, Tahara S, Ohshima K, Kurashige M, Wada N, Morii E. Immunohistochemical analysis of the novel marginal zone B-cell marker IRTA1 in malignant lymphoma. Hum Pathol. 2017;59:70–9. https://doi.org/10.1016/j.humpath.2016.09.011.

Article  CAS  PubMed  Google Scholar 

Jensen MA, Ferretti V, Grossman RL, Staudt LM. The NCI Genomic Data Commons as an engine for precision medicine. Blood. 2017;130(4):453–9. https://doi.org/10.1182/blood-2017-03-735654.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kasajima R, Yamaguchi R, Shimizu E, Tamada Y, Niida A, Tremmel G, Kishida T, Aoki I, Imoto S, Miyano S, Uemura H, Miyagi Y. Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways. Oncol Rep. 2020;43(3):943–52. https://doi.org/10.3892/or.2020.7481.

Article  CAS  PubMed  Google Scholar 

Kassambara A. ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.6.0. 2023. https://CRAN.R-project.org/package=ggpubr.

Levy S, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5: e254.

Article  PubMed  PubMed Central  Google Scholar