An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

This comparison is a challenging task because the sequencing data is discrete while the tiling array data is continuous. We use the published rice and Arabidopsis datasets which provide currently best matched sets of arrays and sequencing experiments using a slightly earlier generation of sequencing, the MPSS tag sequencing technology. After scoring the arrays consistently in both the organisms, a first pass comparison reveals a surprisingly small overlap in transcripts of 22% and 66% respectively, in rice and Arabidopsis. However, when we do the analysis in detail, we find that this is an underestimate. In particular, when we map the probe intensities onto the sequencing tags and then look at their intensity distribution, we see that they are very similar to exons. Furthermore, restricting our comparison to only protein-coding gene loci revealed a very good overlap between the two technologies.Our approach to compare genome tiling microarray and MPSS sequencing data suggests that there is actually a reasonable overlap in transcripts identified by the two technologies. This overlap is distorted by the scoring and thresholding in the tiling array scoring procedure.Although gene expression analysis can reveal interesting clues to the biochemical state of cells, they do not provide a complete picture of cellular transcription as they focus only on known protein-coding genes. There has been considerable interest in the identification and implication of new non-coding RNA molecules in myriad cellular functions [1]. Therefore, it is essential that we use unbiased technologies for transcript mapping to expand our understanding of these classes of RNAs. The introduction of ultra high-throughput next-generation DNA sequencing technologies in the sequencing market at this juncture offers a unique opportunity to develop methods for a fair comparison of data from these technologies.In this work, our objective is to describe an approach towards comparing tiling microarray data a