Based on the alignment results, we identified the set of expressed transcripts and estimated their expression levels.
Combining with previous annotated catalog, we got a full list with 5,576 human lincRNA genes (5,571 known lincRNAs and 5 novel ones, see Methods and Materials for more details) We then estimated their expression levels across 19 wild-type hES samples and 16 normal adult tissue samples with the standard FPKM (Fragments Per Kilobase of transcript per Million mapped reads) index [ 17].
The large number of reads generated from a single sample allow researchers to study the genes being expressed and estimate their expression levels, and to discover alternative splicing and other sequence variations.
Due to the color of the heme in VHb, the VHb-fused target proteins have a red color that provides a visual aid for estimating their expression level and solubility.
The number of reads mapping to miRNAs and their isomiRs were used to estimate their expression levels in the 3 pairs of libraries (SNB-19_siCtrl VS SNB-19_siTDP, SY-5Y_siCtrl VS SY-5Y_siTDP and HT22_siCtrl VS HT22_siTDP).
It ranks the candidate control genes by estimating their expression stability while also taking into account the experimental design (control and disease groups).
Some methods consider that the set of expressed isoforms (Jiang and Wong, 2009) or a candidate superset (Huang et al., 2013; Xing et al., 2006) is known in advance, in which case the only problem is to estimate their expression.
With the advance of next generation sequencing technologies, it is now possible to reconstruct full-length transcripts, estimate their expression levels, and compare the structural and quantitative differences between samples.
The ability to reconstruct full length transcript sequences and accurately estimate their expression levels is widely believed to be critical for unraveling gene functions and transcription regulation mechanisms [ 17].
Not surprisingly, the ability to reconstruct full length isoform sequences and accurately estimate their expression levels is widely believed to be critical for unraveling gene functions and transcription regulation mechanisms [ 3].
This is true both when considering all genes (0.835 < r < 0.958, mean r = 0.913, 0.0362 SD) and when considering only paralogs (0.849 < r < 0.965, mean r = 0.924, 0.0368 SD), indicating that our custom microarray designs accurately distinguish paralogs and estimate their expression levels.
