根据上一步得到的转录因子足迹位点,再结合转录因子的结合motif可以得到每一种转录因子的活性。 转录因子结合motif可以从Plant Transcription Factor Database下载,注意最好整合成一个文件。 输入文件指定从Plant Transcription Factor Database下载的转录因子结合motif的meme文件、第二步得到的转录因子足迹bw文件、基因组序列...
Article 22 July 2021 Base-resolution models of transcription-factor binding reveal soft motif syntax Article 18 February 2021 Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data Article Open access 12 April 2024 Data...
TSS±10kb区的基因，也可以来自已 知公共数据库的注释，如Human Enhancer Disease Database (HEDD)。
# Get a list of motif position frequency matrices from the JASPAR database # 使用getMatrixSet函数从JASPAR数据库中提取Motif的PFM矩阵信息 pfm <- getMatrixSet( x = JASPAR2018, opts = list(species = 9606, all_versions = FALSE) ) # Scan the DNA sequence of each peak for the presence of ...
To explore the related functions of chromatin open state in clear cell renal carcinoma (ccRCC) using the assay for transposase accessible chromatin using sequencing (ATAC-seq) data and transcriptome sequencing (RNA-seq) from The Cancer Genome Atlas (TCGA) database. Peaks of ATAC-seq data were ...
ATAC-Seq技术在间充质干细胞成脂分化早期研究中的应用
We then used WebGestalt (http://www.webgestalt.org) and the functional database OMIM to identify disease-related pathways with enrichment of genes that had islet ATAC-seq peaks with a different prevalence in T2D versus non-diabetic donors. Interestingly, categories including Noninsulin-dependent Diab...
(paired-end and shift-extend) are used. For HMMRATAC, the extended ranges at both sides indicate the nucleosomes. The HINT-ATAC track is footprints detected by HINT-ATAC, while the RUNX1 motif track is the footprints matching RUNX1 motif from JASPAR database. The K562 ChIP-seq track is ...
scRNASeqDB- A database aggregating human single-cell RNA-seq datasets.ref ShinyCortex- a resource that brings together data from recent scRNA-seq studies of the developing cortex for further analysis. ShinyCortex is based in R and displays recently published scRNA-seq data from the human and mo...
1.0>>fpr threshold:0.0001>>>input file pDC loaded:312544regions>>>input file cDC1 loaded:513503regions>>all files loaded>>used database(s):jaspar_vertebrates>>motifs loaded:746>>matching[pDC],312544regions...[297.790seconds]>>matching[cDC1],513503regions...[485.401seconds][total time:0h13...