%0 Journal Article %A Eddie-Luidy Imada %A Diego Fernando Sanchez %A Leonardo Collado-Torres %A Christopher Wilks %A Tejasvi Matam %A Wikum Dinalankara %A Aleksey Stupnikov %A Francisco Lobo-Pereira %A Chi-Wai Yip %A Kayoko Yasuzawa %A Naoto Kondo %A Masayoshi Itoh %A Harukazu Suzuki %A Takeya Kasukawa %A Chung Chau Hon %A Michiel de Hoon %A Jay W Shin %A Piero Carninci %A FANTOM consortium %A Andrew E Jaffe %A Jeffrey T Leek %A Alexander Favorov %A Gloria R Franco %A Ben Langmead %A Luigi Marchionni %T Recounting the FANTOM Cage Associated Transcriptome %D 2019 %R 10.1101/659490 %J bioRxiv %P 659490 %X Long non-coding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes including disease. We present here FC-R2, a comprehensive expression atlas across a broadly-defined human transcriptome, inclusive of over 100,000 coding and non-coding genes as described by the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the original recount2 resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (a) identify tissue specific transcription profiles for distinct classes of coding and non-coding genes, (b) perform differential expression analysis across thirteen cancer types, providing new insights linking promoter and enhancer lncRNAs expression to tumor pathogenesis, and (c) confirm the prognostic value of several enhancers in cancer. Comprised of over 70,000 samples, FC-R2 will empower other researchers to investigate the roles of both known genes and recently described lncRNAs. Access to the FC-R2 atlas is available from https://jhubiostatistics.shinyapps.io/recount/, the recount Bioconductor package, and http://marchionnilab.org/fcr2.html. %U https://www.biorxiv.org/content/biorxiv/early/2019/06/04/659490.full.pdf