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Genes mapped by more than 3 SAGE tags were used as queries.
If any function was mapped by more than 100 targets of tissue-specific miRNAs, then it was selected.
If any pathway was mapped by more than five targets of the tissue-specific miRNAs, then it was selected.
For Unigene clusters mapped by more than one transcript entries, the highest TPM value was used to represent the expression level of the Unigene cluster (van Ruissen et al., 2005).
To complement data from shotgun proteomics and PTM-omics studies discussed in the previous section, PPIs can be directly mapped by more focused sample isolation strategies particularly the use of tandem affinity purification (TAP)–tagged proteins.
Of all the 20,755 unigenes, 26 were uniquely mapped by more than 8,000 reads, which represented the most abundant transcripts in sweetpotato root cDNA library (Additional file 1, Table S1).
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In a fiendishly tricky opening week of a Tour that is beginning to look like it was mapped by scientists more accustomed to testing the intelligence of monkeys, seven teeth-loosening sectors of cobbles were the latest obstacle placed in front of the 191 remaining riders.
To determine the amount of detectable genes, the expression values were averaged for transcripts mapped by 2 or more probes.
Coverage rate was calculated as the percentage of nucleotides in the segment that were mapped by one or more reads (Additional file 1).
On average, 83% of the total reads were successfully mapped by allowing no more than two mismatches and restricting the alignments to at most 40 genomic locations (Additional file 2).
The number of sequences mapped by 1 or more reads (50'541 sequences) exhibited saturation, as a random subset containing 20% of all Illumina reads was sufficient to target 89.5% of them.
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Justyna Jupowicz-Kozak
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