FANTOM

FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM has since developed and expanded over time to encompass the fields of transcriptome analysis. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the ‘elements’ - the transcripts - to an understanding of the ‘system’ - the transcriptional regulatory network, in other words the ‘system’ of an individual life form.

Mouseover and click the image below for more information on the FANTOM history and papers

Simultaneously with producing data, FANTOM established the FANTOM database and the FANTOM full-length cDNA clone bank, which are available worldwide. The FANTOM resources have been used in several important research projects. For instance, the full-length cDNA database was used in a computer prediction of the genomic position (transcriptional unit) of genes by the International Human Genome Sequencing Consortium. Also they have been used by a research group led by Dr. Shinya Yamanaka at Kyoto University, Japan, for establishing Induced pluripotent stem (iPS) cells. In the study, 24 transcription factors were selected from FANTOM database as candidate initiation factors. Furthermore, the Allen Institute for Brain Science in the United State has created a digital atlas that encompasses the whole brain, and has made it publicly available. The atlas graphically illustrates the expression of genes within the mouse brain using Informatix software. This project has also made use of the FANTOM database.

October 2000

FANTOM1 meeting

April 2002

FANTOM2 meeting

September 2004

FANTOM3 main meeting

December 2006

FANTOM4 meeting

October 2011

FANTOM5 meeting

An atlas of combinatorial transcriptional regulation in mouse and man
Ravasi T, Suzuki H, Cannistraci CV, ... Hayashizaki Y
Cell 140, 744-52 (2010)

Genome Biology 10 (2009)
‘BioMed Central Themantic Series: FANTOM4’

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Suzuki H, Forrest ARR, Van Nimwegen E, ... Hayashizaki Y
Nature Genetics 41, 553-562 (2009)

Tiny RNAs associated with transcription start sites in animals
Taft RJ, Glazov EA, Cloonan N, ... Hayashizaki Y, Mattick JS
Nature Genetics 41, 572-578 (2009)

The regulated retrotransposon transcriptome of mammalian cells
Faulkner GJ, Kimura Y, Daub CO, ... Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P
Nature Genetics 41, 563-571 (2009)

Genome-wide analysis of mammalian promoter architecture and evolution
Carninci P, Sandelin A, Lenhard B, ... Hayashizaki Y
Nature Genetics 38, 626-635 (2006)

PLoS Genetics 2, (2006)
‘The Genome Network / FANTOM Collection’

The transcriptional landscape of the mammalian genome
Carninci P, Kasukawa T, Katayama S,... Hayashizaki Y
Science 309, 1559-1563 (2005)

Antisense transcription in the mammalian transcriptome
Katayama S, Tomaru Y, Kasukawa T, ... Hayashizaki Y
Science 309, 1564-1566 (2005)

Genome Research 13 (2003)
‘Special FANTOM Issue’

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Okazaki Y, Furuno M, Kasukawa T, ... Hayashizaki Y
Nature 420, 563-573 (2002)

Functional annotation of a full-length mouse cDNA collection
Kawai J, Shinagawa A, Shibata K, ... Hayashizaki Y
Nature 409, 685-690 (2001)