MEME-ChIP: motif analysis of large DNA datasets.
MEME-ChIP: motif analysis of large DNA datasets.
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DOI：
10.1093/bioinformatics/btr189
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发表时间：
2011-06-15
期刊：
影响因子：
--
通讯作者：
Bailey TL
中科院分区：
文献类型：
--
作者：
Machanick P;Bailey TL
动机：高通量测序的进展导致大型高质量数据集的快速增长，包括转录因子（TF）ChIP-seq实验产生的数据集。虽然有许多现有的工具，发现TF结合位点基序在这样的数据集，大多数基于网络的工具不能直接处理这样的大数据集。结果：MEMEM-ChIP Web服务旨在分析ChIP-seq“峰区域”--宣布的ChIP-seq“峰”周围的短基因组区域。给定一组基因组区域，它执行（i）从头开始基序发现，（ii）基序富集分析，（iii）基序可视化，（iv）结合亲和力分析和（v）基序鉴定。它在输入数据上运行两种互补的基序发现算法-MEME和DREME-并在随后的可视化，结合亲和力和识别步骤中使用它们发现的基序。MEME-ChIP还使用AME算法进行基序富集分析，该算法可以检测具有已知DNA结合基序的TF的结合位点的非常低的富集水平。重要的是，与MEME网络服务不同，对上传序列的大小或数量没有限制，允许分析非常大的ChIP-seq数据集。MEME-ChIP进行的分析为用户提供了ChIP-ed TF的结合和调节活性的各种观点，以及其他DNA结合TF的可能参与。可用性：MEMEME-ChIP作为MEME套件的一部分可在http://meme.nbcr.net上获得。联系方式：t. uq.edu.au补充信息：补充数据可在生物信息学在线获得。
Motivation: Advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (TF) ChIP-seq experiments. While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets. Results: The MEME-ChIP web service is designed to analyze ChIP-seq ‘peak regions’—short genomic regions surrounding declared ChIP-seq ‘peaks’. Given a set of genomic regions, it performs (i) ab initio motif discovery, (ii) motif enrichment analysis, (iii) motif visualization, (iv) binding affinity analysis and (v) motif identification. It runs two complementary motif discovery algorithms on the input data—MEME and DREME—and uses the motifs they discover in subsequent visualization, binding affinity and identification steps. MEME-ChIP also performs motif enrichment analysis using the AME algorithm, which can detect very low levels of enrichment of binding sites for TFs with known DNA-binding motifs. Importantly, unlike with the MEME web service, there is no restriction on the size or number of uploaded sequences, allowing very large ChIP-seq datasets to be analyzed. The analyses performed by MEME-ChIP provide the user with a varied view of the binding and regulatory activity of the ChIP-ed TF, as well as the possible involvement of other DNA-binding TFs. Availability: MEME-ChIP is available as part of the MEME Suite at http://meme.nbcr.net. Contact: t.bailey@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Portales-Casamar E;Thongjuea S;Kwon AT;Arenillas D;Zhao X;Valen E;Yusuf D;Lenhard B;Wasserman WW;Sandelin A
通讯作者：
Sandelin A
影响因子：
3
作者：
McLeay, Robert C.;Bailey, Timothy L.
通讯作者：
Bailey, Timothy L.
DOI：
10.1093/bioinformatics/btq049
发表时间：
2010-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Buske FA;Bodén M;Bauer DC;Bailey TL
通讯作者：
Bailey TL
量化基序之间的相似性。
影响因子：
12.3
作者：
Gupta S;Stamatoyannopoulos JA;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
5.8
作者：
Bailey, TL;Gribskov, M
通讯作者：
Gribskov, M