Motif-based analysis of large nucleotide data sets using MEME-ChIP.
Motif-based analysis of large nucleotide data sets using MEME-ChIP.
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DOI：
10.1038/nprot.2014.083
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发表时间：
2014
期刊：
影响因子：
14.8
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中科院分区：
文献类型：
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MEME-ChIP是一种基于网络的工具，用于分析大型DNA或RNA数据集中的基序。它可以分析ChIP-seq识别的峰区域，cLIP-seq和相关检测识别的交联位点，以及使用其他标准选择的基因组区域集。MEME-ChIP执行从头基序发现、基序富集分析、基序位置分析和基序聚类，提供了输入序列中富集的DNA或RNA基序的全面图片。MEME-ChIP执行两种互补类型的从头基序发现：基于权重矩阵的发现，用于高准确性;基于单词的发现，用于高灵敏度。使用来自人、小鼠、蠕虫、苍蝇和其他模式生物的DNA或RNA基序的基序富集分析提供了甚至更高的灵敏度。MEME-ChIP的交互式HTML输出组和对齐重要的图案，以方便解释。该协议花费不到3小时，并且它提供了与其它在线方法不同且互补的基序发现方法。
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by cLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP’s interactive HTML output groups and aligns significant motifs to ease interpretation. this protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods.