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The eight randomized N-bases were removed prior to alignment. Processed reads were aligned against a custom reference of miRBase hairpins v21 using bowtie v1. Differential expression analysis of miRNA data was performed with R package limma using voom with cyclic loess normalization [ 3033 ]. Median centered normalized log 2 values describing the relative protein abundance in each sample were used for downstream analyses. We explored the msi s1b of in-cis copy number aberrations on gene expression by testing for differences in gene expression among CNA groups. Genes spanning several segments differing in PCF value along the gene were handled as follows: Genes consistently gained or lost different PCF value but belonging to the same category were assigned to the correct category accordingly.
Genes that differed in copy number category e. Only genes represented in all samples were included.
The mRNA expression was defined to be associated with copy number in cis if Wilcoxon testing determined i the mRNA expression to be significantly different in samples with gain versus samples with neutral copy number or loss, or ii the mRNA expression was significantly different in samples with loss versus samples with neutral copy number or gain. We corrected for multiple testing by false discovery rate FDR using the p. Significant genes from in cis analyses were investigated for overlaps with the MSigDB version 5. Associations between CNA and gene expression were additionally assessed by gene-wise Spearman correlations of copy number- and expression values across samples, and genes with correlations above 0.
Results are presented in figures and tables for each individual data level and integration analysis, as summarized in Fig. The cell lines have previously been shown to recapitulate the biological properties of the four CMSs Sveen et al. Colo is derived from a neuroendocrine tumor and has a distinct gene expression profile [ 38 ]. Pin hair as msi s1b and as tight as possible before taking the measurements.
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