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I am working on a study where we performed RNA-seq on multiple xenograft tumor samples (pig tumor cell lines injected into SCID mice). I've used xenome to separate the reads originating from the pig and mouse genomes, and am trying to figure out ways to perform differential expression analysis between the pig reads (tumor) and mouse reads (tumor microenvironment). So far I've performed alignments using STAR and quantifications using RSEM.
Ideally I'd like to perform DEG analysis with DESeq2 or EdgeR based on the RSEM quantification of the orthologous genes, but I'm concerned that is not an appropriate approach to take due to potential differences in gene/genome size and structure. I've been doing literature searches but can't seem to find any publications where gene expression in 1 species is compared to another. Our goal is to identify expression signatures so we can investigate the cross talk between the tumor and tumor microenvironment. Any suggestions people have regarding approaches to do this would be greatly appreciated.
Thanks!
Ideally I'd like to perform DEG analysis with DESeq2 or EdgeR based on the RSEM quantification of the orthologous genes, but I'm concerned that is not an appropriate approach to take due to potential differences in gene/genome size and structure. I've been doing literature searches but can't seem to find any publications where gene expression in 1 species is compared to another. Our goal is to identify expression signatures so we can investigate the cross talk between the tumor and tumor microenvironment. Any suggestions people have regarding approaches to do this would be greatly appreciated.
Thanks!