Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia.
Bioinformatics. 2011 Jun 15;27(12):1696-7. doi: 10.1093/bioinformatics/btr189. Epub 2011 Apr 12.
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.
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.
MEME-ChIP is available as part of the MEME Suite at http://meme.nbcr.net.
高通量测序技术的进步导致了包括转录因子 (TF) ChIP-seq 实验在内的大型、高质量数据集的快速增长。虽然有许多现有的工具可用于在这些数据集中发现 TF 结合位点基序，但大多数基于网络的工具都无法直接处理如此大的数据集。
MEME-ChIP 网络服务旨在分析 ChIP-seq“峰区”——围绕声明的 ChIP-seq“峰”的短基因组区域。给定一组基因组区域，它执行 (i) 从头 motif 发现、(ii) motif 富集分析、(iii) motif 可视化、(iv) 结合亲和力分析和 (v) motif 识别。它在输入数据上运行两个互补的 motif 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 motif。MEME-ChIP 还使用 AME 算法进行 motif 富集分析，该算法可以检测到具有已知 DNA 结合基序的 TF 的结合位点的非常低水平的富集。重要的是，与 MEME 网络服务不同，上传的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 执行的分析为用户提供了 ChIP-ed TF 的结合和调节活性的多种视图，以及其他 DNA 结合 TF 的可能参与。
MEME-ChIP 作为 MEME 套件的一部分在 http://meme.nbcr.net 上提供。
