Gateways to the FANTOM5 promoter level mammalian expression atlas
By M. Lizio, J. Harshbarger, H. Shimoji, Jessica Severin, T. Kasukawa, S. Şahin, I. Abugessaisa, S. Fukuda, Fumi Hori, Sachi Ishikawa-Kato and 31 more. Genome Biology, 2015
820 citations recorded by the source corpus.
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource 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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/f877645e9e6190c1b15c1089b4bd6dc454db5daf
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In Molecular Biology
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Citations in the corpus
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, methodology): “The FAN-TOM5 Consortium utilized the CL as a component of the FANTOM Sample Ontology, in combination with Uberon, the Disease Ontology and the EFO to identify cellular, tissue, disease sources and experimental modifications for the samples used in transcriptional analyses [65].”
- Ensembl 2016 (2015, background): “Gene expression baseline levels are available for a number of studies including FANTOM5 (44) and GTEx (45).”
- The UCSC Genome Browser database: 2019 update (2018, background): “Examples include cis-regulatory annotations created by JASPAR (3), ReMap (4), the Eukaryotic Promoter Database (5), ENCODE(6), the Ensembl regulatory build (7) and Brain and Roadmap Epigenomics (8), RNAs from FANTOM5 (9), Mouse Alleles from MGI (10), lncRNAs from LNCipedia (11), Cancer genomics (sho”
- Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling (2016, background): “Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas.”
- xCell: digitally portraying the tissue cellular heterogeneity landscape (2017, methodology): “Cap Analysis Gene Expression (CAGE) technique [17]; the ENCODE project, from which we annotated 115”