References

Aryee, Martin J, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, and Rafael A Irizarry. 2014. “Minfi: A Flexible and Comprehensive Bioconductor Package for the Analysis of Infinium DNA Methylation Microarrays.” Bioinformatics 30 (10): 1363–69.
Das, Jyotirmoy, Nina Idh, Liv Ingunn Bjoner Sikkeland, Jakob Paues, and Maria Lerm. 2021. “DNA Methylome-Based Validation of Induced Sputum as an Effective Protocol to Study Lung Immunity: Construction of a Classifier of Pulmonary Cell Types.” Epigenetics, 1–12.
Das, Jyotirmoy, Deepti Verma, Mika Gustafsson, and Maria Lerm. 2019. Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.” Epigenetics, April, 1–13. https://doi.org/10.1080/15592294.2019.1603963.
Dedeurwaerder, Sarah, Matthieu Defrance, Emilie Calonne, Hélene Denis, Christos Sotiriou, and François Fuks. 2011. “Evaluation of the Infinium Methylation 450K Technology.” Epigenomics 3 (6): 771–84.
Fortin, Jean-Philippe, Aurélie Labbe, Mathieu Lemire, Brent W Zanke, Thomas J Hudson, Elana J Fertig, Celia MT Greenwood, and Kasper D Hansen. 2014. “Functional Normalization of 450k Methylation Array Data Improves Replication in Large Cancer Studies.” Genome Biology 15 (11): 1–17.
Gillespie, Marc, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, et al. 2021. The reactome pathway knowledgebase 2022.” Nucleic Acids Research 50 (D1): D687–92. https://doi.org/10.1093/nar/gkab1028.
Harrison, Alan, and Anne Parle-McDermott. 2011. “DNA Methylation: A Timeline of Methods and Applications.” Frontiers in Genetics 2: 74.
Houseman, Eugene Andres, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, and Karl T Kelsey. 2012. “DNA Methylation Arrays as Surrogate Measures of Cell Mixture Distribution.” BMC Bioinformatics 13 (1): 1–16.
Johnson, W Evan, Cheng Li, and Ariel Rabinovic. 2007. “Adjusting Batch Effects in Microarray Expression Data Using Empirical Bayes Methods.” Biostatistics 8 (1): 118–27.
Kanehisa, Minoru, and Susumu Goto. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes.” Nucleic Acids Research 28 (1): 27–30. https://doi.org/10.1093/nar/28.1.27.
Khan, Aziz, and Anthony Mathelier. 2017. “Intervene: A Tool for Intersection and Visualization of Multiple Gene or Genomic Region Sets.” BMC Bioinformatics 18 (1): 1–8.
Lacher, DA. 1987. “Interpretation of Laboratory Results Using Multidimensional Scaling and Principal Component Analysis.” Annals of Clinical & Laboratory Science 17 (6): 412–17.
Lacher, David A, and ED O’Donnell. 1988. “Comparison of Multidimensional Scaling and Principal Component Analysis of Interspecific Variation in Bacteria.” Annals of Clinical & Laboratory Science 18 (6): 455–62.
Maksimovic, Jovana, Lavinia Gordon, and Alicia Oshlack. 2012. “SWAN: Subset-Quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips.” Genome Biology 13 (6): 1–12.
Martens, Marvin, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N Slenter, Kristina Hanspers, Ryan A. Miller, et al. 2020. WikiPathways: connecting communities.” Nucleic Acids Research 49 (D1): D613–21. https://doi.org/10.1093/nar/gkaa1024.
Moore, Lisa D, Thuc Le, and Guoping Fan. 2013. “DNA Methylation and Its Basic Function.” Neuropsychopharmacology 38 (1): 23–38.
Mugavin, Marie E. 2008. “Multidimensional Scaling: A Brief Overview.” Nursing Research 57 (1): 64–68.
Pico, Thomas AND van Iersel, Alexander R AND Kelder. 2008. “WikiPathways: Pathway Editing for the People.” PLOS Biology 6 (7): 1–4. https://doi.org/10.1371/journal.pbio.0060184.
Skolnick, Jeffrey, Jacquelyn S Fetrow, and Andrzej Kolinski. 2000. “Structural Genomics and Its Importance for Gene Function Analysis.” Nature Biotechnology 18 (3): 283–87.
Teschendorff, Andrew E, Francesco Marabita, Matthias Lechner, Thomas Bartlett, Jesper Tegner, David Gomez-Cabrero, and Stephan Beck. 2013. “A Beta-Mixture Quantile Normalization Method for Correcting Probe Design Bias in Illumina Infinium 450 k DNA Methylation Data.” Bioinformatics 29 (2): 189–96.
Touleimat, Nizar, and Jörg Tost. 2012. “Complete Pipeline for Infinium Human Methylation 450K BeadChip Data Processing Using Subset Quantile Normalization for Accurate DNA Methylation Estimation.” Epigenomics 4 (3): 325–41.
Triche Jr, Timothy J, Daniel J Weisenberger, David Van Den Berg, Peter W Laird, and Kimberly D Siegmund. 2013. “Low-Level Processing of Illumina Infinium DNA Methylation Beadarrays.” Nucleic Acids Research 41 (7): e90–90.
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.” The Innovation 2 (3): 100141.
Yu, Guangchuang, Li-Gen Wang, Yanyan Han, and Qing-Yu He. 2012. “clusterProfiler: An r Package for Comparing Biological Themes Among Gene Clusters.” Omics: A Journal of Integrative Biology 16 (5): 284–87.

Copyright © 2022-2023. Massimiliano Volpe and Jyotirmoy Das.