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To identify significant differentially expressed transcript tags that distinguished the two groups, we also selected for a fold difference ≥5, a minimal tag count in the corresponding group ≥5 counts, and a P-value≤0.05 resulting in 243 differentially expressed transcripts.
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In addition, a minimal average normalized tag count of 40 TPM was required in the over-expressing dataset.
With the implement of the miRDeep program (Friedlander et al., 2008), NGSmirPlant provides candidate novel microRNAs with the RNA secondary structure, minimal free energy, tag counts of mature/mature* sequence et al. (Fig. 1).
One is based on the total tag count (#specific microRNA tags/ total microRNA sequence tags) and the other is based on the most abundant tag count (#the most abundant tag of specific microRNA/ total microRNA sequence tags).
Table 5 presents an analysis of the tags distribution with respect to the total tag count (and considering service granularity).
This output includes the GSM number, library name, tag count, kinds of tag (with unrepeated tag sequences), total tag count, and TPM.
However the SAGE data were first normalized by dividing each tag count by the total number of tags counted in the library.
aAverage tag count count per individaul tunor SAGE library.
The average tag count for MMP1 was 216 tags and the median 180 tags.
This means that a tag count of 2 from a library of 50,000 tags is equivalent to a tag count of 2 from a library of 200,000 tags.
Percentages displayed are of the total cumulative tag count.
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