Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

@article{Lizio2017UpdateOT,
  title={Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals},
  author={Marina Lizio and Jayson Harshbarger and Imad Eldin Ali Abugessaisa and Shuei Noguchi and Atsushi Kondo and Jessica Severin and Chris J. Mungall and David J. Arenillas and Anthony Mathelier and Yulia A. Medvedeva and Andreas Lennartsson and Finn Drabl{\o}s and Jordan A. Ramilowski and Owen J. L. Rackham and Julian Gough and Robin Andersson and Albin Sandelin and Hans Ienasescu and Hiromasa Ono and Hidemasa Bono and Yoshihide Hayashizaki and Piero Carninci and Alistair R. R. Forrest and Takeya Kasukawa and Hideya Kawaji},
  journal={Nucleic Acids Research},
  year={2017},
  volume={45},
  pages={D737 - D743}
}
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our… 
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
TLDR
The recent updates of both data and interfaces in the FANTOM web resource are reported, including expansion of the resource by employing different assays, which yielded additional atlases of long noncoding RNAs, miRNAs and their promoters.
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs
TLDR
The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs), and the updated FANTOM web resource is publicly available at https://fantom.riken.jp.
FANTOM5 CAGE profiles of human and mouse samples
TLDR
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE coupled with single-molecule sequencing to represent the consequence of transcriptional regulation in each analyzed state of mammalian cells.
Automated methods for cell type annotation on scRNA-seq data
SCSA: a cell type annotation tool for single-cell RNA-seq data
TLDR
SCSA is presented, an automatic tool to annotate cell types from scRNA-seq data, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information.
SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data
TLDR
SCSA is presented, an automatic tool to annotate cell types from scRNA-seq data, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information.
Hierarchical cell type classification using mass, heterogeneous RNA-seq data from human primary cells
TLDR
This work explores the novel application of hierarchical classification algorithms that take into account the graph structure of the Cell Ontology to this task, and trains these algorithms on a novel curated dataset comprising nearly all human public, primary bulk samples in the NCBI’s Sequence Read Archive.
A simple, scalable approach to building a cross-platform transcriptome atlas
TLDR
It is demonstrated that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue, using the open access Stemformatics.org platform.
scDeepHash: An automatic cell type annotation and cell retrieval method for large-scale scRNA-seq datasets using neural network-based hashing
Single-cell RNA-sequencing technologies measure transcriptomic expressions, which quantifies cell-to-cell heterogeneity at an unprecedented resolution. As these technologies become more readily
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA–target interactions
TLDR
With IMOTA (interactive multi omics tissue atlas), this work developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between m RNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens.
...
...

References

SHOWING 1-10 OF 36 REFERENCES
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
TLDR
A web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR), which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project, and demonstrates the utility of the framework for dissemination of large-scale analysis results.
Gateways to the FANTOM5 promoter level mammalian expression atlas
TLDR
The resulting data is assembled into a centralized data resource that contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.
The UCSC Genome Browser database: 2016 update
TLDR
The UCSC Genome Browser has greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.
Mouse genome database 2016
TLDR
The Mouse Genome Database is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease.
[FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones].
The Transcriptional Landscape of the Mammalian Genome
TLDR
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
A promoter-level mammalian expression atlas
TLDR
It is found that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles.
An Integrated Encyclopedia of DNA Elements in the Human Genome
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
An integrated encyclopedia of DNA elements in the human genome
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
...
...