ENCODE TF ChIP-seq data analysis

We downloaded 2,216 ChIP-seq experiment data from the ENCODE Project. The list of the data is in Supplementary Table S8. The data were lifted over from hg19 to hg38. We found overlapping peaks on four different categories: (1) 500bp upstream the promoter region of pcRNA-associated coding genes, (2) 500bp upstream promoter region of pcRNAs, (3) pcRNA genomic loci, and (4) pcRNA genomic loci but not overlapping with promoter region. To understand the correlation of TF binding patterns in the four categories, we made a binary matrix per category that consists of rows of TFs and columns of pcRNA/coding genes. Hence, the matrix contains connections between TF and pcRNA/associate coding genes. The matrix of category 2 is clustered by Euclidian Distance. To check the extent to which promoter sharing or proximity determines TFBS correlation, we also separated the clustered heat-map in the pcRNA bidirectional transcript (BIDIR) subgroup to the other subgroups (Non-BIDIR). To directly compare the TF binding patterns between each category, the other three matrices were sorted by the same order of the clustered matrix. We used the MatLab function corr2 to calculate r-value between category (1) and (2). We performed Monte Carlo simulation to calculate the p-value and test the significance of the r-value. <br>

我们从ENCODE项目（ENCODE Project）中下载获取了2216组染色质免疫共沉淀测序（ChIP-seq）实验数据。该数据集的明细列表详见补充表S8。所有数据均已从hg19基因组版本映射至hg38基因组版本。
我们在四类不同基因组区域中鉴定到了重叠结合峰：(1) 与pcRNA（pcRNA）相关的编码基因启动子区域上游500bp区域；(2) pcRNA的启动子区域上游500bp区域；(3) pcRNA的基因组位点；(4) 不与启动子区域重叠的pcRNA基因组位点。
为探究四类区域中转录因子（Transcription Factor，TF）的结合模式相关性，我们为每一类区域构建了一个二元矩阵：矩阵的行代表TF，列对应pcRNA/编码基因。因此，该矩阵承载了TF与pcRNA/相关编码基因之间的关联关系。
第二类区域对应的矩阵通过欧氏距离（Euclidian Distance）进行聚类分析。
为探究启动子共享或位置邻近对转录因子结合位点（Transcription Factor Binding Site，TFBS）相关性的影响程度，我们将聚类得到的热图划分为pcRNA双向转录本（bidirectional transcript，BIDIR）亚组与非双向转录本（Non-BIDIR）亚组分别开展分析。
为直接对比四类区域的TF结合模式，其余三类矩阵均按照该聚类矩阵的排序顺序进行重排。
我们使用MatLab软件的corr2函数计算了第一类与第二类矩阵之间的相关系数r值。
我们通过蒙特卡洛（Monte Carlo）模拟计算了p值，并对该r值的显著性进行了检验。