Complex Loci in Human and Mouse Genomes
Figure 3
Estimating the Extent and Conservation of Antisense Transcription
(A and B) Estimation of proportion of TUs involved in cis–antisense pairs. Open circles indicate the fraction of all human TUs on the plus strand (A) and all mouse TUs on the plus strand (B) that were found to be involved in cis–antisense pairs when the minus-strand TUs were recomputed starting from random transcript sequence samples of different sizes. Filled circles represent the full datasets based on all available transcript sequences. The saturation curves (see Equation 1) indicated by the lines fit almost perfectly to the sampled data. Fitted human and mouse saturation curves approach 0.45 and 0.43, respectively, as the number of transcript sequences increases, indicating that more than 40% of all TUs might be involved in cis–antisense pairs. Similar estimates were obtained by other sampling approaches (Figure S3).
(C) Estimation of the proportion of human cis–antisense pairs that are conserved in mouse. Open circles indicate the proportion of human cis–antisense pairs found to be conserved in mouse when the full human dataset was compared to mouse datasets recomputed from random mouse transcript sequence samples of different sizes. The same type of saturation curve as in (A) was fitted to the data. Here, a model with c = 1 (i.e., hyperbolic saturation) was preferable as it provided an equally good fit while being simpler. The fitted curve approaches 0.25 as the number of mappings grows, indicating that about 25% of human cis–antisense pairs are conserved in mouse.