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To reduce the false positive rate in our prediction, we have analyzed the position of known ncRNAs in E.coli by classifying all ncRNAs into four classes based on their locations: (i) intergenic; (ii) cds_samestrand; (iii) antisense; and (iv) other cases.
In this study we analyzed the position of the cell cycle regulator gene p21 within the CT of human chromosome 6 (HSA6) upon transcriptional activation.
Having determined the positions of Chromosomes 7, 18 and 19 territories in DLD-1, we analyzed the position of these chromosome territories in nuclei of the three derived cell lines (Figure 2D F).
We analyzed the position of the hippuristanol binding site in the context of a model based on the domain orientation of eIF4AIII in the exon junction complex (EJC) (PDB code 2HYI) [23], [23] (Fig. 1D).
We also analyzed the position of the exon junctions relative to the full-length protein.
Because this particular study analyzed the position of static protein complexes, it provided a more precise mapping than the timing-based studies, but did not by itself characterize the activity of the predicted sites.
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Finally, for insertions and translocations, we analyzed the positioning of anchors versus the reference genome.
As a second measure, we carefully analyzed the positions of the identified YY1 binding motifs within the ORFs of the OLFR genes.
We analyzed the positions of the homozygous SNVs in KR772 and found that these changes do not distribute evenly across the genome.
In addition to histone H3, we also analyzed the positions of the histone H2A variant H2A.Z, which is enriched around TSSs [ 46], and we obtained similar results.
To address this issue, we analyzed the positions of nucleosomes having histone H3 and those having H3K4me3 around broad and peak promoters with and without CpG islands.
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