Fantom5 Transcribed Enhancers In Mm10

<strong>Overview</strong>

Transcribed enhancers were identified and their expression was quantified across all human FANTOM5 libraries, following the re-aligned FANTOM5 CAGE data upon mm10 (GRCm38) (obtained from http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/), and decomposition-based peak identification (obtained from https://zenodo.org/record/545682#.WPuNy1Pyv2Q) by Kawaji, Hideya.

<strong>Description</strong>

Transcribed enhancers were called based on bidirectional balanced RNA signatures as per Andersson et al (2014). Enhancers were only identified distal to known exons (+/-100bp region from boundaries) and transcription start sites (+/-300bp), defined by GENCODE vM7 annotation. In total, 44,138 enhancers were identified across 1,068 libraries and the expression was quantified. For details regarding the identification of transcribed enhancers from CAGE data, please see Andersson et al (2014) and blog post.

Due to varying noise levels across FANTOM5 libraries and the intrinsic low expression levels of transcribed enhancers, library-specific noise levels were estimated to define of robust set of enhancers in each sample. In summary, for each library, expression was quantified in randomly sampled genomic regions distal to assembly gaps, DNase hypersensitive sites (ENCODE), known exons and gene TSSs (GENCODE vM7) to create a genomic background expression distribution. For each library, we called an enhancer active (used) if its expression was above the 99.9th quantile of the library’s genomic background expression distribution. The robust set of enhancers consist of those significantly expressed in at least one library.

While this approach ensures less permissive enhancer calling in noisy libraries, for some libraries the noise threshold is zero meaning that a single CAGE tag is sufficient for calling an enhancer active. Furthermore, the possibility of detecting enhancer transcription is affected by sequencing depth, so the number of active enhancers per library might not be biologically meaningful to compare when sequencing depths differ.

<strong>Data files</strong><br>
Each predicted enhancer is described in BED12 format with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position between blocks of transcription initiation events. Expression and usage matrices are tab delimited and the first row gives the FANTOM5 CNhs IDs and the first column the enhancer ID (same as column 4 in BED file). Usage matrices contain zeroes and ones (0:not used, 1:used).

enhancers (BED12 format)
enhancer expression matrix (tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))
binary enhancer usage matrix (0:not used, 1:used, tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))

概述
本数据集基于经mm10（GRCm38）版本重新比对的FANTOM5 CAGE（Cap Analysis of Gene Expression，帽分析基因表达）数据（获取自http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/），以及Kawaji与Hideya开发的基于分解的峰识别方法（获取自https://zenodo.org/record/545682#.WPuNy1Pyv2Q），在全部人类FANTOM5文库中鉴定了转录增强子（transcribed enhancers），并对其表达量进行定量。

数据描述
转录增强子的鉴定依据Andersson等人（2014）提出的双向平衡RNA特征。仅在GENCODE vM7注释定义的已知外显子（边界上下游±100bp区域）和转录起始位点（上下游±300bp区域）的远端区域鉴定增强子。最终在1068个文库中共鉴定出44138个增强子并完成表达定量。如需了解从CAGE数据中鉴定转录增强子的详细方法，请参考Andersson等人（2014）的研究及相关博客文章。

由于FANTOM5各文库的噪声水平存在差异，且转录增强子本身表达量较低，因此我们通过估算文库特异性噪声水平，以定义每个样本中的可靠增强子集合。简言之，针对每个文库，我们在组装间隙、DNase超敏感位点（ENCODE数据库）、已知外显子及基因转录起始位点（GENCODE vM7注释）的远端区域随机采样基因组区域，以此构建基因组背景表达分布。对于每个文库，若某增强子的表达量高于该文库基因组背景表达分布的99.9分位数，则将其判定为活跃（已使用）增强子。本数据集的可靠增强子集合为至少在一个文库中显著表达的增强子。

尽管该方法可降低噪声文库中增强子的鉴定宽松度，但部分文库的噪声阈值为0，即仅需1个CAGE标签即可判定增强子为活跃状态。此外，增强子转录的检测成功率受测序深度影响，因此当测序深度存在差异时，不同文库的活跃增强子数量可能不具备生物学层面的比较意义。

数据文件
所有预测得到的增强子均以BED12格式进行描述，其中两个区块分别代表负链和正链上转录起始区域的合并区域。thickStart与thickEnd列代表转录起始事件区块之间的推断中点位置。表达矩阵与使用矩阵均为制表符分隔格式：第一行为FANTOM5的CNhs编号，第一列为增强子ID（与BED文件第4列一致）。使用矩阵仅包含0和1两个数值（0代表未使用，1代表已使用）。

- 增强子文件（BED12格式）
- 增强子表达矩阵（制表符分隔，第一行：CNhs编号，第一列：增强子ID（坐标））
- 二元增强子使用矩阵（0：未使用，1：已使用，制表符分隔，第一行：CNhs编号，第一列：增强子ID（坐标））