ROSE的bin文件夹下有以下脚本: ROSE_bamToGFF.py ROSE_callSuper.R ROSE_geneMapper.py ROSE_main.py 我们call enhancer主要用ROSE_main.py,具体用法如下: ROSE_main.py -g HG38 -i ${id}.narrowPeak.bed -r ${id}_H3K27AC.deduplicate.chr.bam -c ${id}_H3K27AC_INPUT.deduplicate.chr.bam -o ...
Super enhance,SE,即超级增强子,是一类具有超强转录激活特性的DNA顺式调控元件,该概念由Whitehead Institute for Biomedical Research的学者Richard A. Young 于2013年首次提出,并曾预言“超级增强子具有广阔的研发前景和价值,必将成为下一个药物研发的黄金靶点!” 与普通增强子(Typical enhancer, TE)相比,超级增强子具有如...
找蛋白HIF1a结合在基因nos1附近,与super enhancer重叠的motif 一、先说一下rose( RANK ORDERING OF SUPER-ENHANCERS) 定义一下super enhancer(SE),https://en.wikipedia.org/wiki/Super-enhancer,通用H3K27ac的chip-seq macs2出来的bed,通过rose筛选出来的enhancer_withsuper.bed。 安装方法如下: 点击查看安装方法...
both in vitro and in vivo (Fig.1d). For example, research in leukemia demonstrated that the SEs adjacent to theMYCgene comprised multiple enhancer modules, each exhibiting unique activity levels. By employing dual sgRNAs in conjunction with Cas9 mRNA to systematically delete these elements, it wa...
the enhancer activity is vitrificated through a dual luciferase reporter assay after constructing the plasmid.dCRISPR/Cas9 constructs containing specific small guide RNAs (sgRNAs) targeting the enhancer region are constructed to assess the function of SE by individually depleting each element.eThe CRISPR...
Table 1 High-throughput sequencing involved in super-enhancer omics Full size table A computerized algorithm called “Rank Ordering of Super-Enhancers” (ROSE) was developed to predict SEs based on ChIP-seq signal in 2013 [6]. This algorithm stitches together enhancers located within a certain dis...
Super-enhancer regions were identified using the Rank Order Super-Enhancer (ROSE) algorithm [34] (Fig. 5a). Our analysis determined 403 super-enhancer regions in 10A, 627 in AT1, 1053 in DCIS, and 320 in CA1 cells (Additional file 8: Table S5). Interestingly, a stepwise increase in ...
To identify super-enhancers a 褋VM-based analysis of the ChIP-seq binding patterns of the active enhancer-associated mark is employed. The use of the proposed method is described step-by-step: configuration of cVM; ChIP-seq data alignment; peak calling; ROSE algorithm; interpretation of the ...
column 1: chromosome (chr#) column 2: unique ID for each constituent enhancer region column 4: start of constituent column 5: end of constituent column 7: strand (+,-,.) column 9: unique ID for each constituent enhancer region NOTE: if value for column 2 and 9 differ, value in column...
into one group to capture dense enhancer clusters [32]; (3) Identifying super-enhancers. ROSE algorithm (http://younglab.wi.mit.edu/super_enhancer_code.html) is a tool for finding SEs using gff file (regions of enhancer) and bam file (the factor density of enhancers). After ranking stit...