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Initial assignment of identified sequences to the subfamilies was done separately for every species in a following way.
This study presents the first comprehensive mapping of TSS and assignment of identified promoter sequences to σ factors in an α-proteobacterium.
Assignment of identified genes to superordinate biological processes (Falsig et al. 2006), and if possible to key events of adverse outcome pathways (Bal-Price et al. 2015) or other toxicological mechanisms (Grinberg et al. 2014), is an important step from data generation to increased toxicological information.
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The FunCat 01 (Metabolism) was comprised of 178.5 standardized functional assignments of identified ESTs, making it the most highly represented functional category.
After assignment of the identified genes to KEGG pathways, we found that there were no common pathways among the 21 gene deletions shared by the H1, CH-ES1 and 2102Ep cells.
Assignment of the identified proteins to functional categories was also done for dormancy breaking in water, and in the presence of ABA and GA (Fig. 3).
To allow the assignment of the identified TSS to their putative origin, an allocation to four different classes was accomplished [ 34].
Mapping of individual fragments was done by a series of inter-fragment PCRs and by 3'- and 5'-RACE-PCRs, confirming the initial assignment of the identified fragments to six genes.
Since the transformed E-value [ 37] now may serve as a common statistical standard across different search methods, one may wish to understand how the statistical significance assignment of the identified peptides is impacted by using a convoluted spectrum.
The assignment of phosphorylation sites of identified phosphopeptides was performed by the PTM scoring algorithm implemented in MSQuant as described previously [31].
Those cut offs would lead to false positive assignments (NC) or the loss of identified true positive domains (TC), respectively.
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