Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq (original) (raw)
Figure 7
Analyses of allele-specific expression.
(A) An example of a heterozygous locus identified from genomic Roche 454 reads (horizontal bars). Colors represent alignments in the forward and reverse directions. The arrow indicates a heterozygous locus. (B) Density plots of allelic expression ratios calculated from simulated reads and RNA-seq reads. The black and red lines correspond to simulated reads containing 0.01 and 0.02 errors/base. The blue line represents RNA-seq data (GS isolate). (C) Histogram of allele ratios (genomic) of heterozygous loci. The superimposed curve (brown) shows the density of the underlying data. The allele ratio was calculated from genomic reads as the fraction of allele A among allele A+B. Grey bars represent loci containing two presumed copies of each allele and blue bars three copies (or vice versa) of each allele. (D) Boxplots of allele expression ratios (y-axis) according to the allele ratio (x-axis). The black line of each box is the median. Dots represent outliers. (E) Allelic Expression Ratios of heterozygous loci of the same haplotype phase. Each dot represents one pair of linked heterozygous loci (SNP pairs). The allelic expression of SNPs 1 and 2 are shown on the x- and y-axes. Red dots indicate discordant heterozygous loci and black dots represent concordant heterozygous loci; i.e., the direction of gene expression change is the same.