Department of Gene and Cell Medicine and The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA.
Wiley Interdiscip Rev Syst Biol Med. 2010 Nov-Dec;2(6):708-33. doi: 10.1002/wsbm.93.
Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multi-layered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature.
近年来，对胚胎干细胞（ES 细胞）进行系统分析的努力已经产生了大量的高通量数据。此外，新兴的数据库和计算工具也促进了 ES 细胞的研究，并进一步为包括多个分子层的调控网络的计算机重建铺平了道路。在这里，我们简要地调查了用于组织和分析为研究哺乳动物细胞系统（重点是 ES 细胞）而收集的高通量实验数据的数据库、算法和软件工具。讨论了使用异构数据来重建完整的多层次 ES 细胞调控网络的设想。本综述还提供了一个配套的手动提取数据集，其中包含来自低通量实验 ES 细胞研究的不同类型的调控相互作用，可在 http://amp.pharm.mssm.edu/iscmid/literature 上获得。
