Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

By T. Shiraki, S. Kondo, S. Katayama, K. Waki, T. Kasukawa, H. Kawaji, Rimantas Kodzius, A. Watahiki, Mari Nakamura, T. Arakawa and 7 more. 2003

820 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era (2012, background): “Note however that all three collections which are partly or exclusively based on CAGE data show a mono-modal TATA-box peak whereas ENSEMBL shows a multi-modal distribution, suggesting that many gene starts annotated in ENSEMBL do not correspond to a true TSS.”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, neutral): “Successful RACE reactions (%) Index TF 5' RACE 3' RACE 5' and 3' RACE 5' or 3' RACE Transcription on both strands No transcript detected Exonic 20 19 (95) 19 (95) 16 (80) 20 (100) 19 (95) 0 (0) Intronic 90 71 (79) 77 (86) 66 (73) 79 (88) 65 (72) 11 (12) Intergenic 90 62 (69) 65 (72) 44 (49) 77 (86) ”
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools (2014, methodology): “In the early 2000s, novel high-throughput protocols were invented for comprehensive TSS mapping of a whole transcriptome at once (4,5).”
GENCODE: producing a reference annotation for ENCODE (2006, background): “In addition, other technologies such as mapping RNA to tiling arrays [27], cap analysis gene expression (CAGE) tags [28], and gene identification signature (GIS) ditags [29] indicate there is transcriptional activity outside the regions currently annotated by the GENCODE consortium.”
Next-Generation Genomics: an Integrative Approach (2010, neutral): “1 ) with methods for the capture of the 5′ ends of genes (such as cap analysis of gene expression (CAGE) tag”
CpG islands and the regulation of transcription. (2011, neutral): “Air is a noncoding RNA (ncRNA) that initiates at a CGI within intron 2 of Igf2r and is essential for silencing of the paternal allele (Sleutels et al. 2002).”
Genome-wide analysis of mammalian promoter architecture and evolution (2006, methodology): “To increase the depth of coverage, we have carried out systematic 5′-end analysis of the mouse and human transcriptome using the cap analysis of gene expression (CAGE) approac”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, neutral): “The decreased background for GRO-cap results in part from differences in the methodologies (cap-trapping 29 versus the oligo-capping method 30 ) used to capture capped transcripts.”
RNA sequencing: advances, challenges and opportunities (2010, methodology): “One of the first high-throughput TSS mapping methods was the cap analysis of gene expression (CAGE) approach, which was initially developed for Sanger sequencin”