A Promoter-level mammalian expression atlas

Th FANTOM Consortium, A Promoter-level mammalian expression atlas, Nature 507, 2014

Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find 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.

FANTOM5 project has performed cap analysis of gene expression (CAGE) across 975 human and 399 mouse samples, including primary cells, tissues and cancer cell lines, using single-molecule sequencing.

We have identified and quantified the activity of at least one promoter for more than 95% of annotated protein-coding genes in the human reference genome.

Promoter-based expression data also has direct practical applications in the interpretation (and re-interpretation) of the function of single nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS), which commonly occur in non-coding genes.

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