Figure 2.

Summary of differentially expressed in vitro and in vivo foci transcriptomes using Cuffdiff and Sleuth. (A) Depicts a heat map of normalized FPKM comparing RNA-seq datasets from the Giardia grown in in vitro culture (TYDK) to Giardia transcriptomes associated with the in vivo foci excised from the proximal small intestine (pSI) (see Figure 1). For clarity, only differentially expressed genes confirmed by two independent methods are summarized by the heat map, with red indicating highly expressed genes, and blue indicating low expressed genes. Differentially expressed transcripts in the in vitro (TYDK) and in vivo (foci) datasets were identified by the concordance of two computational methods (B). Overlap in both upregulated and downregulated genes in the in vivo transcriptomes was calculated and is shown in (C). The asterisk indicates the 475 differentially upregulated genes (187 total) and downregulated genes (288 total) that were concordant between both methods. Of the 475 concordant differentially expressed genes, the 25 most highly transcribed genes present in the in vitro (D) and in vivo foci transcriptomes (E) are also ranked (FPKM). Underlined genes are those that are among the 25 most highly transcribed genes in both the in vitro and the in vivo transcriptome datasets.