title: Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
abstract: The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release.
authors.affiliation: RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan. kawaji@gsc.riken.jp
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Marina
authors.initials: M
authors.lastname: Lizio
authors.forename: Alistair R R
authors.initials: AR
authors.lastname: Forrest
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.forename: Michael
authors.initials: M
authors.lastname: Rehli
authors.forename: Kate
authors.initials: K
authors.lastname: Schroder
authors.forename: Katharine
authors.initials: K
authors.lastname: Irvine
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Carsten O
authors.initials: CO
authors.lastname: Daub
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D045744:Cell Line, Tumor; D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D020407:Internet; D008264:Macrophages / Q000378:metabolism; D051379:Mice; D058977:Molecular Sequence Annotation; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors