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Thus, selective use of TSS may be a mechanism to regulate expression under different conditions.
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The different use of TSSs has also previously been shown to be a mean of regulation.
This indicates that a large fraction of the isoforms arise from differential use of TSSs or TTSs.
Our next three complexity measures were based on the number of transcripts that are generated due to alternative use of TSSs, alternative splicing, and alternative polyadenylation, respectively.
In particular, our study revealed for the majority of protein-coding genes the use of TSSs downstream the ATG start codons.
We then considered complexity in terms of alternative isoforms generated by differential use of TSSs (fig. 2 C ), splice sites (fig. 2 D ), and polyadenylation sites (fig. 2 E ).
We have made some use of RAMPAGE TSS data (Batut et al. 2013), which are drawn from a complete range of developmental stages, and will soon make more systematic use of that dataset.
To assess whether AS or use of alternative TSS could alter the function of the predicted protein, we compared the GO functional categories of the Type A and Type B (Table 2).
However, the TSS information used in these analyses was downloaded from known database and was not based on the use of real TSSs identified within each examined library.
The use of internal TSSs greatly increases the transcriptomic complexity and regulatory capacity [ 22, 86].
However, in recent years, new insights into the regulation of gene expression became available, showing among other things a frequent use of alternative TSSs.
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