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

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

Hideya Kawaji  1 , Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair R R Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub
Affiliations

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

Hideya Kawaji et al. Genome Biol. 2009.

Abstract

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.

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Figures

Figure 1
Figure 1
CD11b activity. Microarray-based expression and CAGE-based promoter activities of CD11b, a monocytic marker gene.
Figure 2
Figure 2
Overview of the FANTOM web resource. The FANTOM4 data and the other CAGE tags are collected in the FANTOM web resource, which consists of the genome browser interface and data files.
Figure 3
Figure 3
Genome browser interface. Details about the items displayed in the genome browser can be inspected with several parallel pop-up windows. Microarray-based gene expression is displayed in a horizontal bar plot. Promoter activities along with THP-1 time course and different tissues are displayed as a vertical bar plot and a heatmap table, respectively.
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