Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY 10029, USA.
Database (Oxford). 2013 Jun 21;2013:bat045. doi: 10.1093/database/bat045. Print 2013.
High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE
越来越多的研究团队利用转录组学和蛋白质组学等各种全基因组技术来描绘小鼠和人类胚胎干细胞（m/hESCs）的特征，但整合这些数据以获得 m/hESCs 中分子电路的整体视图的工作却相对滞后。在这里，我们介绍了一个名为“从多能性证据看胚胎干细胞图谱”（Embryonic Stem Cell Atlas from Pluripotency Evidence）的 m/hESC 为中心的数据库，该数据库整合了来自多个最近的高通量研究的数据，包括染色质免疫沉淀测序（chromatin immunoprecipitation followed by deep sequencing）、全基因组抑制性 RNA 筛选（genome-wide inhibitory RNA screens）、基因表达微阵列（gene expression microarrays）或关键因子敲低（knockdown，KD）或过表达（overexpression）后的 RNA-seq、免疫沉淀结合质谱蛋白质组学和磷酸化蛋白质组学。该数据库提供了基于网络的交互式搜索和可视化工具，可用于构建子网络，并识别各种调控层中的已知和新的调控相互作用。网络界面还包括通过滑块控制的加性效应预测组合 KD 的效果的工具，或者通过在 MATLAB 中实现的模拟软件。总的来说，“从多能性证据看胚胎干细胞图谱”数据库是干细胞系统生物学社区的一个综合性资源。数据库网址：http://www.maayanlab.net/ESCAPE
