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Fig. 2 | Genome Biology

Fig. 2

From: Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity

Fig. 2

iSINE-containing transcripts are less expressed in ENCODE datasets. a, b RNA-seq data for 15 different human cell lines available from the ENCODE project were analyzed and the expression level (FPKM fragments per kilobase of transcript per million mapped reads) was determined. Subsequently, the transcripts were sorted according to the presence or absence of Alu elements in exonic regions or the orientation of Alu elements. Shown is a pool of transcripts from all 15 cell lines grouped into seven categories: all = all transcripts, single = exactly one Alu element per transcript, iAlu = Alu elements in inverted orientation, head-head/tail-tail = Alu elements in sense/antisense or antisense/sense orientation, tandem = Alu elements in tandem orientation, no Alu = transcripts not containing any Alu. Horizontal numbers in the individual bars indicate the average FPKM for each class of transcript whereas the vertical numbers indicate the total number of transcripts found for each category in all 15 cell lines. b The statistical significance of differences in expression between gene sets was tested using the nonparametric Wilcoxon rank-sum test (two-sided and one-sided)

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