Abstract
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.
Highlights
This year marks the 20th year from the first publication by the Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium, where biology, genomics and bioinformatics experts from all over the world collaborated in providing the first collection and functional annotation of more than one million full-length mouse cDNAs [1]
We assessed the functional implications of the 340 targeted individual antisense oligos (ASOs) by performing differential gene expression, Motif Activity Response Analysis (MARA) [21], and Gene Set Enrichment Analysis (GSEA) [22]
The FANTOM web resource has been updated by (i) adding computationally predicted resources of motif activity; genomewide transcription factor binding sites (TFBS) and multiple genome alignments for human, mouse, chicken, rat and macaque; (ii) reprocessing of the existing atlases and datasets based on the latest-available genome assemblies; (iii) further curating metadata for FANTOM5 sample ontologies; and (iv) enhancing existing web applications and user interfaces
Summary
This year marks the 20th year from the first publication by the FANTOM Consortium, where biology, genomics and bioinformatics experts from all over the world collaborated in providing the first collection and functional annotation of more than one million full-length mouse cDNAs [1]. We provide new non-coding RNA (ncRNA) resources including the functional annotation of 285 human lncRNAs from the FANTOM6 pilot study [8], along with the miRNA atlases of rat, dog, chicken and macaque [19].
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