Сибатов Р.Т., Саенко Ю.В., Учайкин В.В., Саенко В.В., Морозова Е.В., Шулежко В.В., Кожемякина Е.В., Бызыкчи А.Н., Гусаров Г.Г., Коробко Д.А., Яровикова И.В., Салтыкова К.В., Кожемякин И.И., Журавлев В.М., Журавлев А.В., Айнуллова Н.К.
Cтатистический анализ радиационно-индуцированной динамики транскриптома раковых клеток по данным ДНК-микроматриц
Математическая биология и биоинформатика. 2013;8(2):520-528.
doi: 10.17537/2013.8.520.
Список литературы
- Schena M. Microarrays: biotechnology's discovery platform for functional genomics. Trends in Biotechnology. 1998;16(7):301-306. doi: 10.1016/S0167-7799(98)01219-0
- Young RA. Biomedical discovery with DNA arrays. Cell. 2000;102(1):9-15. doi: 10.1016/S0092-8674(00)00005-2
- Butte A. The use and analysis of microarray data. Nature Reviews Drug Discovery. 2002;1(12):951-960. doi: 10.1038/nrd961
- Slonim DK. From patterns to pathways: Gene expression data analysis comes of age. Nature Genetics. 2002;32:502-508. doi: 10.1038/ng1033
- Stafford P. Methods in Microarray Normalization. CRC Press; 2008. doi: 10.1201/9781420052794
- Lim WK, Wang K, Lefebvre C, Califano A. Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics. 2007;23(13):i282-i288. doi: 10.1093/bioinformatics/btm201
- Affymetrics Inc. Statistical algorithms description document. 2013. http://www.affymetrics.com/support/technical/whitepapers.affx (accessed 31 July 2013).
- 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 Biology. 2004;5(10):R80:1-R80:16.
- Gautier L, Cope L, Bolstad BM, Irizarry RA. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307-315. doi: 10.1093/bioinformatics/btg405
- Smith CA. Browser-based Affymetrix Analysis and Annotation. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer; 2005. P. 313-326. doi: 10.1007/0-387-29362-0_18
- Smyth GK. Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer; 2005. P. 397-420. doi: 10.1007/0-387-29362-0_23
- Gentleman R, Carey V, Huber W, Hahne F. Genefilter: methods for filtering genes from microarray experiments. Version 1.42.0. 2013. http://www.bioconductor.org/ packages/2.12/bioc/manuals/genefilter/man/genefilter.pdf (accessed 31 September 2013).
- http://media.affymetrix.com/support/developer/powertools/changelog/gcos-gcc/cel (accessed 31 September 2013).
- Garrett-Mayer E. Overview of Standard Clustering Approaches for Gene Microarray Data Analysis. In: DNA Microarrays and Related Genomics Techniques Design, Analysis, and Interpretation of Experiments. Eds. D.B. Allison, G.P. Page, T.M. Beasley, J.W. Edwards. Taylor & Francis Group, LL; 2006.
- Liu M, Wang G, Gomez-Fernandez CR, Guo S. GREB1 functions as a growth promoter and is modulated by IL6/STAT3 in breast cancer. PLoS One. 2012;7(10):e46410. doi: 10.1371/journal.pone.0046410
- He G, Sun D, Ou Z, Ding A. The Protein Zfand5 binds and stabilizes mRNAs with AU-rich elements in their 3′-untranslated regions. Journal of Biological Chemistry. 2012;287(30):24967-24977. doi: 10.1074/jbc.M112.362020
- Skinner HD, Sandulache VC, Ow TJ, Meyn RE, Yordy JC, Beadle BM, Fitzgerald AL, Giri U, Ang KK, Myers JN. TP53 Disruptive Mutations Lead to Head and Neck Cancer Treatment Failure through Inhibition of Radiation-Induced Senescence. Clinical Cancer Research. 2012;18(1):290-300. doi: 10.1158/1078-0432.CCR-11-2260
- Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185-193. doi: 10.1093/bioinformatics/19.2.185
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