Projects FANTOM

FANTOM1 (Functional Annotation of the Mammalian Genome 1) launched by RIKEN. Created the first comprehensive full-length cDNA clone collection from the mouse genome, establishing the foundation for mammalian transcriptome annotation.

Construction of the mouse full-length cDNA encyclopedia, generating over 60,000 full-length cDNA clones. Represented the most comprehensive collection of mammalian full-length cDNAs at the time, enabling systematic annotation of the mouse transcriptome.

FANTOM3 transcript annotation producing the mouse gene catalog based on physical cDNAs. Extended the cDNA collection and provided comprehensive transcript annotation, distinguishing protein-coding from non-coding RNAs and revealing the complexity of the mammalian transcriptome.

Systematic description of the FANTOM5 data collection, including CAGE profiling of 975 human and 152 mouse samples, transcription factor expression data, and the Zenbu genome browser interface. Data series underpinning the mammalian transcriptome atlases.

Major update of the FANTOM web resource, expanding to provide additional transcriptome atlases including FANTOM5 CAGE data, FANTOM6 lncRNA functional data, and improved tools for browsing and analyzing promoter/enhancer expression across cell types.

FANTOM enters its 20th year with expanded transcriptomic atlases including FANTOM6 functional annotation of non-coding RNAs. The resource now covers CAGE-based expression for over 2,000 samples and provides extensive functional data on lncRNAs through systematic perturbation screens.

Flagship FANTOM5 paper: comprehensive promoter-level expression atlas across 975 human and 152 mouse samples using CAGE (Cap Analysis of Gene Expression) sequencing. Identified and quantified promoter usage across diverse cell types, revealing the core promoter architecture of the mammalian genome.

Review of the FANTOM projects and their paradigm-shifting contributions to genomics, including the transition from cDNA-based transcript annotation to CAGE-based promoter/expression analysis, and the discovery of widespread non-coding RNA transcription.

Comprehensive atlas of 27,919 human long non-coding RNA (lncRNA) genes with accurate 5' ends defined by CAGE. Provided a high-confidence catalog of lncRNAs with detailed annotation of their expression patterns, conservation, and genomic features across diverse cell types.