Abstract
The objectives of this chapter are to teach generating DEGs in microarray gene expression data, extracting a gene cluster of genes with similar patterns of expression, classifying the observed data using SVM and KNN, and learning the basic syntax of the R program, a useful tool for genome data analysis.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
BCR/ABL fusion gene, cytogenetically normal, and ALL1/AF4 fusion gene.
Bibliography
Chiaretti S et al (2004) Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood 103(7):2771–2778
Eisen MB et al (1998) Cluster analysis and display of genome-wide expression patterns. PNAS 95(25):14863–14868
Gentleman R (2016) Annotate: annotation for microarrays. R package version 1.52.1
Gentleman R, Carey V, Huber W, Hahne F (2016) genefilter: genefilter: methods for filtering genes from high-throughput experiments. R package version 1.56.0
Golub T (2016) golubEsets: exprSets for golub leukemia data. R package version 1.16.0
Huber W et al (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18(suppl 1):S96–S104
Li X (2009) ALL: a data package. R package version 1.16.0
Meyer D, Dimitriadou E, Hornik K, Weingessel A, Leisch F (2017) e1071: misc functions of the department of statistics, probability theory group (formerly: E1071), TU Wien. R package version 1.6-8. https://CRAN.R-project.org/package=e1071
Tamayo P et al (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. PNAS 96(6):2907–2912
Tibshirani R, Chu G, Narasimhan B, Li J (2011) samr: SAM: Significance analysis of microarrays. R package version 2.0. https://CRAN.R-project.org/package=samr
Venables WN, Ripley BD (2002) Modern applied statistics with S, 4th edn. Springer, New York. ISBN 0-387-95457-0
Yan J (2016) som: Self-Organizing Map. R package version 0.3-5.1. https://CRAN.R-project.org/package=som
Author information
Authors and Affiliations
1 Electronic Supplementary Material
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Kim, J.H. (2019). Gene Expression Data Analysis. In: Genome Data Analysis. Learning Materials in Biosciences. Springer, Singapore. https://doi.org/10.1007/978-981-13-1942-6_6
Download citation
DOI: https://doi.org/10.1007/978-981-13-1942-6_6
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-1941-9
Online ISBN: 978-981-13-1942-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)