Serial analysis of gene expression gives exceptionally unbiased transcriptional data because it is based on extraction of unique sequence tags for each distinct transcript, known or unknown, differentially expressed or not, from a population of transcripts.
Such research has been facilitated by the commercial availability of standardized microarrays such as the Affymetrix GeneChip® Tiling Array Set 1.0R which provides 35-bp probe spacing of 45 million oligonucleotide probes which can be used for unbiased RNA transcript mapping.
The genomic distribution profiles of the 'ultra-high density' probes, like standard tiling arrays including the NimbleGen CGH arrays, are essentially linear and unbiased unlike most transcript arrays which are biased towards the 3′ end of transcripts and sometimes overlap [ 19].
More recently, the availability of RNAseq data has provided a new store of unbiased data on transcript expression.
The redundancy and depth of coverage of 454 pyrosequencing also provides and unbiased representation of transcript abundance, which is useful for relative gene expression analysis especially in non-model plants that lack complete genome sequence information [ 33, 34].
On the other hand, purifying selection on male-biased genes only appears to be stronger than selection on unbiased genes when transcript abundance levels are not taken into account, suggesting that preferential conservation of male-biased genes on the neo-Y is mainly a consequence of their higher expression levels in males (table 2).
This approach has a number of caveats, for example, it assumes unbiased sampling of transcripts.
In A. thaliana, pyrosequencing has been tested successfully to verify whether this technology is able to provide an unbiased representation of transcripts as compared to the sequenced genome.
That said, current estimates of transcriptome coverage and the impacts of multiplexing strategies analysed in this paper assume unbiased sampling of transcripts.
We demonstrate that for both SAGE and Affymetrix GeneChips the intra-platform correlations are extremely good, but that the inter-platform agreement based on an unbiased selection of transcripts is modest.
