Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

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Serval ID
serval:BIB_41C692308C7B
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Journal
Nucleic Acids Research
Author(s)
Kawaji H., Severin J., Lizio M., Forrest A.R., van Nimwegen E., Rehli M., Schroder K., Irvine K., Suzuki H., Carninci P., Hayashizaki Y., Daub C.O.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2011
Volume
39
Number
Database issue
Pages
D856-D860
Language
english
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.
Keywords
Animals, Cell Differentiation/genetics, Cell Line, Tumor, Computer Graphics, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, Genomics, Humans, Internet, Macrophages/metabolism, Mice, Molecular Sequence Annotation, Transcription Factors/metabolism, Transcription, Genetic, User-Computer Interface
Pubmed
Web of science
Open Access
Yes
Create date
27/10/2011 13:58
Last modification date
20/08/2019 13:42
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