The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Genome Biol. 2009;10(4):R40. doi: 10.1186/gb-2009-10-4-r40. Epub 2009 Apr 19.


In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation / methods
  • Databases, Genetic*
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Humans
  • Information Storage and Retrieval / methods
  • Internet*
  • MicroRNAs / genetics
  • Oligonucleotide Array Sequence Analysis / methods
  • RNA, Messenger / genetics
  • RNA, Small Interfering / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic / genetics*
  • User-Computer Interface


  • Chromatin
  • MicroRNAs
  • RNA, Messenger
  • RNA, Small Interfering
  • Transcription Factors