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In fact, only 3.3%% of cancer-related SNPs ultimately lead to a change in amino acid at the protein level, while more than 80%% of SNPs map to expressed non-coding regions [ 44].
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An average of 85% of the clean reads mapped to expressed unigenes.
The gene models for the 71 high quality candidates were manually checked and errors in the predicted gene coding regions were corrected by mapping to expressed sequence tags (ESTs) [ 20] or according to well-characterized features of P. sojae introns, e.g., most introns are between 60 and 90 bp, and begin with GT and end with AG [ 21].
"We chose data mapping to express this experience in an unconventional way," explains Klapper.
To compare our results to a recent SILAC study looking at the effects of global changes upon deletion of rpd3, over 60% of the proteins quantified in this study map to differentially expressed peptides in that report.
A large proportion of our reads mapped to these expressed loci (>93%), indicating that they include a good representation of the expressed portion of the wheat genome.
In principle, a one-to-one mapping of reconstructed transcripts to expressed transcripts could be achieved by finding pairs of equal transcripts between the expressed transcripts and the assembled transcripts.
Modules that are identified in the gene layer for entire sample set are mapped to their expressed proteins.
Furthermore, a Chi-square test confirmed that the amount of reads mapped to highly expressed genes (>1000x) did not follow the same distribution than those mapped to the bulk of genome (p<1e-8).
Another technological achievement the combined use of reverse transcription, PCR, and automated sequencing to map expressed genes led to administrative changes at the NIH when, in April 1992, Watson resigned from his position as director of the NCHGR following a conflict with NIH director Bernadine Healy over gene patenting.
Another interesting application is to map differentially expressed genes to the SuperGenome and then to find out whether some of these map to 'regions of interest', such as pathogenicity islands.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com