Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
Bioinformatics. 2011 Mar 1;27(5):715-7. doi: 10.1093/bioinformatics/btq707. Epub 2010 Dec 23.
CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators.
CompleteMOTIFs（cMOTIFs）是一个集成的网络工具，旨在方便从高通量染色质免疫沉淀实验中系统地发现转录因子结合基序的重复出现。对多个峰位置的全面注释和布尔逻辑操作使用户能够使用 MEME、Weeder 和 ChIPMunk 等工具专注于感兴趣的基因组区域进行从头开始的基序发现。该流水线整合了来自 TRANSFAC 和 JASPAR 数据库的已知基序扫描工具，并使用局部或预先计算的背景模型进行富集测试，这显著提高了基序扫描结果。此外，我们使用 cMOTIFs 流水线证明，多个转录因子可以协同结合到重要干细胞分化调节剂的上游。
