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When available, target genes identified using high-throughput CLIP data were collected from the supplemental materials of the corresponding studies (Lipchina et al., 2011; Loeb et al., 2012; Helwak et al., 2013; Grosswendt et al., 2014).
This implies miRNA targets identified from PAR-CLIP data are more likely to be in a protein complex from the CORUM database (12%) as compared to proteins in general (2%).
GO analyses of DEGs and PAR-CLIP data were performed using DAVID.
55% of the proteins with miRNA targets sites predicted based on PAR-CLIP data were moderately down-regulated (log2-fold change < -0.1).
As a result of the study, a set of background binding events in PAR-CLIP data is publicly available in GEO (GSE50989).
In PIPE-CLIP, the data are pre-processed to remove noise such as the PCR duplicates.
For all these reasons, computational approaches, designed specifically to deal with CLIP-seq data, are important in this field.
HITS-CLIP data have been deposited in GEO under accession number GSE47794.
RNA-seq and HITS-CLIP data have been deposited to the Gene Expression Omnibus under the accession numbers GSE53779 and GSE58381.
We intended to obtain unpublished data for subgroup analysis (coiling vs. clipping), but no additional data are available to construct the subgroup analysis.
The parameters used for the OM-OFDM transmission are given in Table 5. OM-OFDM, OFDM, and clipped OFDM data were sent through a 5-tap typical-urban area by using the parameters previously mentioned.
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