Ji Xuwo, Li Wei, Song Jun, Wei Liping, Liu X Shirley
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, People's Republic China 100871.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W551-4. doi: 10.1093/nar/gkl322.
The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP-chip experiments to locate the in vivo-binding sites of transcription factors in the human genome and explore the regulatory mechanisms. Once genomic regions enriched by transcription factor ChIP-chip are located, genome-scale downstream analyses are crucial but difficult for biologists without strong bioinformatics support. We designed and implemented the first web server to streamline the ChIP-chip downstream analyses. Given genome-scale ChIP regions, the cis-regulatory element annotation system (CEAS) retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes and identifies enriched transcription factor-binding motifs. Biologists can utilize CEAS to retrieve useful information for ChIP-chip validation, assemble important knowledge to include in their publication and generate novel hypotheses (e.g. transcription factor cooperative partner) for further study. CEAS helps the adoption of ChIP-chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is http://ceas.cbi.pku.edu.cn.
近期高密度人类基因组平铺阵列的出现，使生物学家能够开展染色质免疫沉淀芯片（ChIP-chip）实验，以定位人类基因组中转录因子的体内结合位点，并探索调控机制。一旦通过ChIP-chip确定了富含转录因子的基因组区域，对于没有强大生物信息学支持的生物学家来说，全基因组规模的下游分析至关重要但却困难重重。我们设计并实现了首个用于简化ChIP-chip下游分析的网络服务器。给定全基因组规模的ChIP区域，顺式调控元件注释系统（CEAS）可检索重复序列屏蔽的基因组序列、计算GC含量、绘制进化保守性图谱、定位附近基因并识别富集的转录因子结合基序。生物学家可利用CEAS检索用于ChIP-chip验证的有用信息，整合重要知识以便在其发表成果中纳入，并生成新的假设（如转录因子合作伙伴）以供进一步研究。CEAS有助于在哺乳动物系统中采用ChIP-chip，并为更全面地理解转录调控机制提供见解。该服务器的网址为http://ceas.cbi.pku.edu.cn。
