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== Paper:== *Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers, http://www.sciencemag.org/content/331/6017/593.full *Some notes from the supplementary on gene expression and satellite expression profiling 1) Reads were aligned to a custom made library for the mouse major satellite sequence from UCSC genome browsere 2) Reads aligning to the repeat reference were counted and their fraction of the total number of genome aligned reads was determined 3) Gene expression counts were determined based on alignments to the annotated transcriptomes based on a statistical gene counting method 4) Gene counts were normalized per million aligned genomic reads for all samples 5) For linear correlation of mouse major satellite to transcriptome, linear regression analysis of the normalized expression levels of each gene across all tissues vs the measured satellite expression level. 6) Genes were then ranked according to decreasing Pearson coefficient and a set of highly correlating genes (R>0.85) was selected for further analysis.
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