Figure 2. Cross-species analysis of gene expression in cultured skin fibroblasts.

(A) Pipeline to obtain the species-specific ortholog sets and expression values. See Materials and methods or a more detailed description of the methodology. (B) Sequence identity of ortholog sets compared to mouse. Nucleotide and amino acid sequence identity of the ortholog sets in each species was compared to mouse reference (mouse was set as 100%). The ortholog sequences were based on de novo assembled transcriptomes, as well as NCBI genomes (if available; indicated by ‘#’). The box plot shows the distribution across the 9389 gene orthologs, with the central bars indicating median values. (C) Read alignment rates for mapping to complete genomes and ortholog sets. Percent of total reads that could be uniquely aligned to the complete genomes (if available, indicated by ‘#’; shaded bars) or to the ortholog sets are shown. Error bars refer to standard error of mean. Number of samples (biological and technical replicates) per species is indicated in parenthesis.

DOI: http://dx.doi.org/10.7554/eLife.19130.004

Figure 2—figure supplement 1. Quality assessment of orthologs.

(A) Percentage of ortholog sets filled up using consensus. Horizontal axis indicates the percentage of sequence length filled up by consensus. For example, 74% of the ortholog sets did not require filling up or were filled up <10% of the sequence length. Five percent of the ortholog sets were filled up 90–100% of the sequence length. (B) Standardized expression values of ortholog sets filled up using consensus. Within each ortholog set, the expression values were standardized to mean = 0 and standard deviation = 1. Distribution of the median pairwise DNA distance among (C) the Mouse Reference orthologs and (D) the expressed orthologs. The DNA distanced is based on Kimura 2- parameters distance.

DOI: http://dx.doi.org/10.7554/eLife.19130.005