2018
DOI: 10.1093/nar/gky917
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CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals

Abstract: High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA–protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise—different extent of non-specific interactions caused by individual transcript abundance—that has been inconsiderately normalized, resulting in sacrifice of sensitivity. To properly deconvolute RNA–protein interactions, we have implemented CLIPick, a … Show more

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Cited by 9 publications
(9 citation statements)
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“…
Figure 1 AGO CLIP analyses identified putative anticancer miRNAs associated with HPV18 in cervical cancer (A) AGO CLIP performed in HeLa cells, a cell line derived from a cervical cancer patient with HPV18 infection (left panel). AGO-bound regions on which AGO CLIP reads were reproducibly mapped between biological replicates (biological complexity [BC] ≥ 2, CLIPick 12 ) are represented on the HPV18 reference genome (GenBank: NC_001357 ; right panel). Detailed mapping statistics can be found in Figure S1 A.
…”
Section: Resultsmentioning
confidence: 99%
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“…
Figure 1 AGO CLIP analyses identified putative anticancer miRNAs associated with HPV18 in cervical cancer (A) AGO CLIP performed in HeLa cells, a cell line derived from a cervical cancer patient with HPV18 infection (left panel). AGO-bound regions on which AGO CLIP reads were reproducibly mapped between biological replicates (biological complexity [BC] ≥ 2, CLIPick 12 ) are represented on the HPV18 reference genome (GenBank: NC_001357 ; right panel). Detailed mapping statistics can be found in Figure S1 A.
…”
Section: Resultsmentioning
confidence: 99%
“…Of note, TCGA data were normalized by median RPM of all expressed miRNAs due to the lack of normal cervix data. (C) AGO-bound regions (BC ≥ 2, CLIPick 12 ) mapped in HPV18 transcripts, including E6 and E7, following annotation of the reference genome (upper panel) or E6/E7 transcript expressed in HeLa cells (GenBank: M20324 ; lower panel), of which the 3ʹ end of E7 was fused with the host genome (blue shading; hg19, chr8:128,240,800–128,241,377). Seed sites of miRNAs in the identified cluster (green shading in B) were mapped with indication of their positions in seeds.…”
Section: Resultsmentioning
confidence: 99%
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