This protocol provides detailed instructions on Quality Control, EWAS, and CpG island signature discovery with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip data. R package minfi and caret was used in this analysis.
Video created by Johns Hopkins University for the course "Bioconductor for Genomic Data Science". In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi Learn online and earn valuable credentials from top ...
This protocol provides detailed instructions on Quality Control, EWAS, and CpG island signature discovery with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip data. R package minfi and caret was used in this analysis.
The development and progression of cancer(1-3) and the experimental reversal of tumorigenicity(4,5) are accompanied by complex changes in patterns of gene expression. Microarrays of cDNA provide a powerful tool for studying these complex phenomena
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective minimum criterion for cell cycle regulation. In separate experiments, designed to examine the effects of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins. Furthermore, we analyzed our set of cell cycle-regulated genes for known and new promoter elements and show that several known elements (or variations thereof) contain information predictive of cell cycle regulation. A full description and complete data sets are available at http://cellcycle-www.stanford.edu
N. Ali, M. Shaheen, M. Mabrouk, and M. AboRezka. International Journal of Computer Science & Information Technology (IJCSIT), 12 (5):
01 - 18(October 2020)