在作者团队之前的研究中,ChRBP gawky是胁迫诱导转录过程中的特异性调控因子。为了阐释gawky调控与被调控的完整通路,在本研究中,作者通过CLIP-Seq及分子生物学实验,鉴定出一类铜胁迫过程中与ChRBP gawky特异性结合且富含金属响应元件的circRNA(metal-responsive element-containing circRNA, MRE circRNA)。circRNA-Seq及核质...
EuRBPDB还整合了837个交联免疫沉淀(CLIP)序列(CLIP-seq)数据集,使用户能够分析RBPs的RNA靶标。尽管数据库和其他数据库取得了进步,但仍然严重缺乏探索RBP功能所需的关键信息。例如,尽管已经报道了许多RBPs,但这些数据库中大多数RBPs的RNA...
新型CLIP技术让RBP-RNA互作研究化繁为简 紫外交联免疫共沉淀(CLIP)是一种用于研究RNA结合蛋白(RNA bindingprotein, RBP)-RNA互作关系的技术。通过将此技术与高通量测序(CLIP-Seq)结合,可以在全转录组范围内鉴定出特定RBP-RNA互作网络,对于RNA转录后调控研究意义非凡。 CLIP技术首先利用紫外照射将RBP与RNA耦联,再使用...
2022年8月4日,清华大学杨雪瑞团队在Genome Biology上在线发表题为“Survey of the binding preferences of RNA-binding proteins to RNA editing events”的研究论文,该研究利用ENCODE项目的RNA-seq和RBP eCLIP-seq数据集,定量调查了150个R...
By integrating vast amounts of data generated by technologies such as RNA-Seq and CLIP-Seq, researchers can identify RBP binding sites at the whole genome level, analyze RBP binding patterns, and their functions in different biological processes. This information helps to reveal the mechanisms of ...
seCLIP-seq发现了STAT3这个转录因子与NORAD lncRNA的直接相互作用 摘要: 胚胎干细胞的自我更新和细胞命运决定被广泛的分子信号所驱动。尽管已经有很多研究探讨了人胚胎干细胞(hESCs,下同)中的转录调节因子,RNA结合蛋白(RBP,下同)对于人的多能性的作用还不清楚。所以作者通过蛋白组学筛选发现了hESCs中的810个结合RNA的...
However, these CLIP-seq data still cannot provide the full view of the RBP binding landscape, it is because CLIP-seq relies on gene expression which can be highly variable between experiments. But these big data can serve as training data for machine learning models to predict missing RBP ...
Shiny App for the visualisation of RBP-RNA interactions supported by the binding sites of RBPs derived from CLIP-seq data (ENCORI database). clip-seqggplotrbpshinyapprbp-rna UpdatedMar 15, 2024 R Online attendance checker with nfc cards. ...
点击P,search RBP,包括了ENCODE的eCLIP-seq数据和其他已发表的PAR-CLIP、HITS-CLIP、iCLIP和PIP-seq数据。 例如查询RBP TAF15 在ENCODE的eCLIP-seq数据中,发现TAF15靶向如下基因的RNA TAF15调控的基因富集在哪些GO生物学过程和KEGG pathway。 鉴于help里对GO和KEGG版本的描述,建议下载靶基因列表,用注释最新的...
GraphProt2 utilizes RBP binding sites identified by CLIP-seq and related protocols to train a graph convolutional neural network (GCN) based model. The model is then used to predict new binding sites on given input RNA sequences. The following figure illustrates the GraphProt2 framework and its...