title: Deep Cap Analysis of Gene Expression (CAGE): Genome-Wide Identification of Promoters, Quantification of Their Activity, and Transcriptional Network Inference.
abstract: Among the most significant findings of the post-genomic era, the discovery of pervasive transcription of mammalian genomes has tremendously modified our understanding of the genome output seen as RNA molecules. The increased focus on non-protein-coding genomic regions together with concomitant technological innovations has led to rapid discovery of numerous noncoding transcripts (ncRNAs). Biological relevance and functional roles of the vast majority of these ncRNAs remain largely unknown.The cap analysis of gene expression (CAGE) technology allows accurate transcript detection and quantification without relying on preexisting transcript models. In combination with complementary data sets, generated using other technologies, it has been shown as an efficient approach for exploring transcriptome complexity.Here, we describe the use of CAGE for the identification of novel noncoding transcripts in mammalian cells providing detailed information for basic data processing and advanced bioinformatics analyses.
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland. Alexandre.Fort@unige.ch.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Fort
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Fish
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D011401:Promoter Regions, Genetic; D012315:RNA Caps; D015203:Reproducibility of Results; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012315:RNA Caps
keywords: Cap Analysis of Gene Expression (CAGE); Noncoding RNAs; Transcription start sites (TSSs); Transcriptomics