References

Cancer Genome Atlas Research Network, John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, and Joshua M Stuart. 2013. “The Cancer Genome Atlas Pan-Cancer Analysis Project.” Nat. Genet. 45 (10): 1113–20.

Chen, Xin, Ang Li, Bao-Fa Sun, Ying Yang, Ya-Nan Han, Xun Yuan, Ri-Xin Chen, et al. 2019. “5-Methylcytosine Promotes Pathogenesis of Bladder Cancer Through Stabilizing mRNAs.” Nat. Cell Biol. 21 (8): 978–90.

Colaprico, Antonio, Tiago C Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais S Sabedot, et al. 2016. “TCGAbiolinks: An R/Bioconductor Package for Integrative Analysis of TCGA Data.” Nucleic Acids Res. 44 (8): e71.

Fouad, Hanan, Hosni Salem, Doha El-Sayed Ellakwa, and Manal Abdel-Hamid. 2019. “MMP-2 and MMP-9 as Prognostic Markers for the Early Detection of Urinary Bladder Cancer.” J. Biochem. Mol. Toxicol. 33 (4): e22275.

Gallo, Cristian A, Rocio L Cecchini, Jessica A Carballido, Sandra Micheletto, and Ignacio Ponzoni. 2016. “Discretization of Gene Expression Data Revised.” Brief. Bioinform. 17 (5): 758–70.

Hahsler, Michael, Sudheer Chelluboina, Kurt Hornik, and Christian Buchta. 2011. “The Arules R-Package Ecosystem: Analyzing Interesting Patterns from Large Transaction Data Sets.” J. Mach. Learn. Res. 12 (57): 2021–25.

Han, A L, B A Veeneman, L El-Sawy, K C Day, M L Day, S A Tomlins, and E T Keller. 2017. “Fibulin-3 Promotes Muscle-Invasive Bladder Cancer.” Oncogene 36 (37): 5243–51.

Imoto, Seiya, Sun Yong Kim, Hidetoshi Shimodaira, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, and Satoru Miyano. 2002. “Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression.” Genome Inform. 13: 369–70.

Kamimura, Takeshi, Hidetoshi Shimodaira, Seiya Imoto, Sun Yong Kim, Kousuke Tashiro, Satoru Kuhara, and Satoru Miyano. 2003. “Multiscale Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression.” Genome Inform. 14: 350–51.

Killian, Theo, and Laurent Gatto. 2021. “Exploiting the DepMap Cancer Dependency Data Using the Depmap R Package.” F1000Res. 10 (416): 416.

Kuhn, Max. 2008. “Building Predictive Models in R Using the Caret Package.” Journal of Statistical Software, Articles 28 (5): 1–26.

Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Genome Biol. 15 (12): 550.

Robin, Xavier, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez, and Markus Müller. 2011. “pROC: An Open-Source Package for R and s+ to Analyze and Compare ROC Curves.” BMC Bioinformatics 12 (March): 77.

Sales, Gabriele, Enrica Calura, Duccio Cavalieri, and Chiara Romualdi. 2012. “Graphite - a Bioconductor Package to Convert Pathway Topology to Gene Network.” BMC Bioinformatics 13 (January): 20.

Scutari, Marco. 2010. “Learning Bayesian Networks with the Bnlearn R Package.” Journal of Statistical Software, Articles 35 (3): 1–22.

Vasala, Kaija, Paavo Pääkkö, and Taina Turpeenniemi-Hujanen. 2003. “Matrix Metalloproteinase-2 Immunoreactive Protein as a Prognostic Marker in Bladder Cancer.” Urology 62 (5): 952–57.

Winerdal, Malin E, David Krantz, Ciputra A Hartana, Ali A Zirakzadeh, Ludvig Linton, Emma A Bergman, Robert Rosenblatt, et al. 2018. “Urinary Bladder Cancer Tregs Suppress Mmp2 and Potentially Regulate Invasiveness.” Cancer Immunol Res 6 (5): 528–38.

Wu, Tianzhi, Erqiang Hu, Shuangbin Xu, Meijun Chen, Pingfan Guo, Zehan Dai, Tingze Feng, et al. 2021. “clusterProfiler 4.0: A Universal Enrichment Tool for Interpreting Omics Data.” Innov. J., July, 100141.

Yu, Guangchuang, and Qing-Yu He. 2016. “ReactomePA: An R/Bioconductor Package for Reactome Pathway Analysis and Visualization.” Mol. Biosyst. 12 (2): 477–79.