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首页> 外文期刊>RNA >Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles
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Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles

机译：SETEN：一种系统鉴定和比较与RNA结合蛋白质相关的过程，表型和疾病的工具，来自条件特定的夹SEQ型材

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RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein RNA interaction landscape at single-nucleotide resolution in a cell, currently there are very few tools that can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps. Here, we present Seten, a web-based and command line tool, which can identify and compare processes, phenotypes, and diseases associated with RBPs from condition-specific CLIP-seq profiles. Seten uses BED files resulting from most peak calling algorithms, which include scores reflecting the extent of binding of an RBP on the target transcript, to provide both traditional functional enrichment as well as gene set enrichment results for a number of gene set collections including BioCarta, KEGG, Reactome, Gene Ontology (GO), Human Phenotype Ontology (HPO), and MalaCards Disease Ontology for several organisms including fruit fly, human, mouse, rat, worm, and yeast. It also provides an option to dynamically compare the associated gene sets across data sets as bubble charts, to facilitate comparative analysis. Benchmarking of Seten using eCLIP data for IGF2BP1, SRSF7, and PTBP1 against their corresponding CRISPR RNA-seq in K562 cells as well as randomized negative controls, demonstrated that its gene set enrichment method outperforms functional enrichment, with scores significantly contributing to the discovery of true annotations. Comparative performance analysis using these CRISPR control data sets revealed significantly higher precision and comparable recall to that observed using ChIP-Enrich. Seten's web interface currently provides precomputed results for about 200 CLIP-seq data sets and both command line as well as web interfaces can be used to analyze CLIP-seq data sets. We highlight several examples to show the utility of Seten for rapid profiling of various CLIP-seq data sets. Seten is available on http://wwvv.iupuledu/similar to sysbio/seten/.
机译：RNA结合蛋白（RBPS）通过与其同源RNA结合，控制在转录后水平的真核基因组中的基因表达调节。虽然目前可以使用夹子（交联和免疫沉淀）协议的几种变体以在细胞中的单核苷酸分辨率下研究全球蛋白质RNA相互作用景观，但目前有很少的工具可以促进理解和解剖RBP的功能关联结果绑定图。在这里，我们呈现SETEN，基于Web和命令行工具，其可以识别和比较与RBPS相关的过程，表型和疾病从条件特定的剪辑-SEQ配置文件。 SETEN使用由大多数峰呼叫算法产生的床文件，包括分数反映RBP在靶转录物上的结合程度，以提供传统的功能性富集以及基因设定的许多基因集合，包括生物陶诗， Kegg，反应组，基因本体论（GO），人类表型本体（HPO），以及用于几种生物的Malacards疾病本体论，包括果蝇，人，小鼠，大鼠，蠕虫和酵母。它还提供了一种选择动态地将数据集的相关基因集与气泡图动态比较，以便于比较分析。使用Eclip数据对IGF2BP1，SRSF7和PTBP1的Eclip数据进行基准测试，并在K562细胞中的相应CRISPRNA-SEQ以及随机性阴性对照中表明，其基因设定富集方法优于功能性富集，分数显着促进了真实的发现注释。使用这些CRISPR控制数据集的比较性能分析显示了使用芯片丰富观察到的精度明显高的精度和相当的召回。 SETEN的Web界面当前提供预先计算的结果有关大约200剪辑-SEQ数据集，并且可以使用命令行以及Web接口来分析剪辑SEQ数据集。我们突出显示了几个例子，以显示SETEN的实用程序，以便为各种剪辑-SEQ数据集的快速分析。 seten可在http：//wwvv.iupuledu/similar与sysbio / seten /。

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