Kawaji, Hideya and Severin, Jessica and Lizio, Marina and Forrest, Alistair R. R. and van Nimwegen, Erik and Rehli, Michael and Schroder, Kate and Irvine, Katharine and Suzuki, Harukazu and Carninci, Piero and Hayashizaki, Yoshihide and Daub, Carsten O. (2011) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. NUCLEIC ACIDS RESEARCH, 39. D856-D860. ISSN 0305-1048,
Full text not available from this repository. (Request a copy)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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | LEUKEMIA-CELL-LINE; FUNCTIONAL ANNOTATION; GENE-EXPRESSION; GENOME BROWSER; SITES; ATLAS; MOUSE; IDENTIFICATION; DATABASE; THP-1; |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Lehrstuhl für Innere Medizin III (Hämatologie und Internistische Onkologie) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 01 Jul 2020 09:00 |
| Last Modified: | 01 Jul 2020 09:00 |
| URI: | https://pred.uni-regensburg.de/id/eprint/21639 |
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