Directed Chemical Evolution with an Outsized Genetic Code
Fig 5
The plots show the number of RRSFL encoding genes (y-axis) contained within the top N total genes (x-axis) of a list ranked by enrichment ratio. If the gene ranking had been perfect, the curves would have gone straight up the y-axis and then cut right on the x-axis at the top of the plot. The solid black line shows how RRSFL genes accumulate at a 90% false discovery rate (i.e. when every tenth gene is a hit). The y-value at the intersection of each curve with the solid black line corresponds to the number of RRSFL genes that would have been detected below a 90% false discovery threshold. A. Improved gene ranking over successive generations. The number of RRSFL genes at the top of ranked lists from the zeroth (yellow), second (red), third (green) and fourth (blue) generations is shown. None of the RRSFL genes could be detected below a 90% false discovery threshold in the zeroth or second generations, whereas 207 and 505 out of 1296 total could be detected in the third and fourth generations respectively. B. Dependence of gene ranking on sequencing depth. The effect of using increasingly small fractions of the total sequencing data to rank genes is shown. 505, 416, 319 and 188 of the RRSFL genes could be detected below a 90% false discovery threshold given 3 million, 1.5 million, 0.75 million and 0.3 million sequencing reads respectively. The discovered fraction of RRSFL genes grew roughly in proportion to the square root of the number of reads. C. Improved gene ranking with a redundant genetic code. The ranking of RRSFL gene sets based on 187500 gene reads and a two codon-per- amino acid genetic code is shown. In one case, the reads used for the analysis were restricted to genes containing a single codon from each codon pair. In this single-codon case, 32 of the 81 RRSFL genes sets could be detected below a 90% false discovery threshold. Alternatively, an identical number of gene reads were used for the analysis, but the reads included genes containing both codons of each codon pair. In the two-codon case, 58 of the 81 RRSFL genes sets could be detected. The two-codon genetic code revealed 70% of the RRSFL gene sets, while the one-codon code revealed only 40%.