Refining Whole Transcriptome Analysis of Plasmodium falciparum Genetic Crosses

Like most organisms, Plasmodium falciparum phenotypes are driven by the regulation of transcription. Study of differential gene expression identify genes and the mechanisms behind phenotypes of interest, such as drug resistance. However, the analysis of transcriptional data in P. falciparum is heavily confounded by unusual cyclical patterns of expression observed in the apicomplexan parasites. This body of work describes a complete, detailed approach to transcriptional analysis of a newly derived P. falciparum genetic cross, and the tools used to perform these analyses. This approach includes a detailed analysis of the parental transcriptional time courses, a novel application of a correctional method for the cyclic nature of transcription, and a detailed solution for the difficulties of data curation and analysis of expression Quantitative Trait Locus analysis in P. falciparum.