Toward a complete in silico, multi-layered embryonic stem cell regulatory network

Wiley Interdiscip Rev Syst Biol Med. Nov-Dec 2010;2(6):708-33. doi: 10.1002/wsbm.93.

Abstract

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.

Publication types

  • Review

MeSH terms

  • Algorithms
  • Databases, Factual
  • Embryonic Stem Cells / metabolism*
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs / metabolism
  • Phosphorylation
  • RNA Interference
  • RNA, Messenger / metabolism
  • Signal Transduction

Substances

  • MicroRNAs
  • RNA, Messenger