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

Kawaji, H. and Severin, J. and Lizio, M. and Forrest, A. R. and van Nimwegen, E. and Rehli, M. and Schroder, K. and Irvine, K. and Suzuki, H. and Carninci, P. and Hayashizaki, Y. and Daub, C. O.. (2011) Update of the FANTOM web resource : from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39 (1 Supplement). D856-D860.

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Official URL: http://edoc.unibas.ch/dok/A5842442

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:10 Oct 2017 08:45
Deposited On:08 Jun 2012 06:51

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