ArticleNucleic acids research2011
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- A MicroRNA Network ControlsmBio · 2020Article
- Regulation of miR-1-Mediated Connexin 43 Expression and Cell Proliferation in Dental Epithelial Cells.Frontiers in cell and developmental biology · 2020Article
- Benchmark and integration of resources for the estimation of human transcription factor activities.Genome research · 2019Article
- Analysis of impact metrics for the Protein Data Bank.Scientific data · 2018Article
- Neat-en-ing up our understanding of p53 pathways in tumor suppression.Cell cycle (Georgetown, Tex.) · 2018Review
- RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.Nucleic acids research · 2017Article
- Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes.BMC genomics · 2017Article
- The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.Nucleic acids research · 2017Article
- Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.Nucleic acids research · 2017Article
- Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform.Open biology · 2016Article
- Evolution of the unspliced transcriptome.BMC evolutionary biology · 2015Article
- Short stories on zebrafish long noncoding RNAs.Zebrafish · 2014Review
- Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.Genome biology · 2014Article
- Dissecting the chromatin interactome of microRNA genes.Nucleic acids research · 2014Article
- 5meCpG epigenetic marks neighboring a primate-conserved core promoter short tandem repeat indicate X-chromosome inactivation.PloS one · 2014Article
- Functional transcriptomics in the post-ENCODE era.Genome research · 2013Article
- MicroRNA-144 is regulated by activator protein-1 (AP-1) and decreases expression of Alzheimer disease-related a disintegrin and metalloprotease 10 (ADAM10).The Journal of biological chemistry · 2013Article
- Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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