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Out of the transgene-expressing founders, we chose those showing highest Venus expression for further breeding, i.e. VLV A1 and A3 as well as VV A9 and A19.
Therefore, we focused on pRKIP expression for further analyses.
These criteria identified N = 95 genes with sufficient, and sufficiently variable, gene expression for further analysis.
We chose the LjPAL1 promoter, which shows typical differential expression, for further analysis.
Due to the role of p16 in cell cycle, we selected only the cases with strong nuclear p16 expression for further HPV typing by DNA analysis.
Although LV rescue and TDM are standard for HDMTX regimens, and folate and B12 supplementation is standard for pemetrexed to increase MTD, new strategies will include pharmacogenetic markers such as tumoral TYMS expression for further improvement of antifolate treatment.
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Since cDNA microarray alone could be subject to errors through cross-hybridization, the gene expressions for further study should be validated using new RNA samples [ 13].
To overcome these weaknesses, a Monte Carlo logic regression (MCLR) approach is designed [ 12], which partly incorporates Bayesian model selection techniques and reports a group of plausible Boolean expressions for further investigation.
To prepare the gene expression matrix for further downstream analysis, we applied a KNN (k = 10) imputation to make sure an expression value existed for all genes in all samples [ 57].
To increase the accuracies of the measured expression levels for further analyses, data from two biological replicates were merged, and FPKM values were calculated based on the merged dataset.
This method provides a tool which can be used for the amplification of all genes of the H1N1 and H3N2 subtypes of influenza A virus prior to analysis of their sequences, and to construct expression plasmids for further study.
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