title: CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.
abstract: Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high resolution and functional significance, published CAGE data are still underused in promoter analysis due to the absence of tools that enable its efficient manipulation and integration with other genome data types. Here we present CAGEr, an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform. Crucially, we provide collections of TSSs derived from most published CAGE datasets, as well as direct access to FANTOM5 resource of TSSs for numerous human and mouse cell/tissue types from within R, greatly increasing the accessibility of precise context-specific TSS data for integrative analyses. The CAGEr package is freely available from Bioconductor at http://www.bioconductor.org/packages/release/bioc/html/CAGEr.html.
authors: Department of Biology, University of Bergen, Thormøhlensgate 53 A & B, N-5008 Bergen, Norway Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
authors: Vanja
authors: V
authors: Haberle
authors: RIKEN Center for Life Science Technologies, Division of Genomic Technologies (CLST DGT), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors: Alistair R R
authors: AR
authors: Forrest
authors: RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors: Yoshihide
authors: Y
authors: Hayashizaki
authors: RIKEN Center for Life Science Technologies, Division of Genomic Technologies (CLST DGT), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors: Piero
authors: P
authors: Carninci
authors: Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Høyteknologisenteret, Thormøhlensgate 55, N-5008 Bergen, Norway b.lenhard@imperial.ac.uk.
authors: Boris
authors: B
authors: Lenhard
mesh_terms: D000818:Animals; D057225:Data Mining; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D051379:Mice; D011401:Promoter Regions, Genetic; D012984:Software; D013737:Testis / Q000196:embryology / Q000378:metabolism; D024363:Transcription Initiation Site
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