CAGE: cap analysis of gene expression

By Rimantas Kodzius, M. Kojima, Hiromi Nishiyori, Mari Nakamura, S. Fukuda, M. Tagami, D. Sasaki, K. Imamura, C. Kai, M. Harbers and 2 more. Nature Methods, 2006

506 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8399564cbc47b08bb0765ecbbfa1ac7429e2eac0

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Vladimir B. Bajic
2. Claes Wahlestedt
3. Mihaela Zavolan
4. John S. Mattick

In Molecular Biology

1. Wyeth W. Wasserman
2. Albin Sandelin
3. Boris Lenhard
4. Wenqiang Shi
5. Yifeng Li
6. Sean M. Grimmond
7. Vladimir B. Bajic
8. Claes Wahlestedt

Citations in the corpus

• Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, methodology): “The cap analysis of gene expression (CAGE) technique [23] captures the 5’-end of RNA transcripts, enabling a precise determination of transcript initiation sites.”
• ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014, background): “next-generation sequencing data of 5’ ends of mRNAs [1, 2], and the 5’ ends of all known mRNAs listed in GenBank.”
• Genome-wide analysis of mammalian promoter architecture and evolution (2006, background): “Results Defining TSSs by CAGE tags CAGE tags are 20- or 21-nt sequence tags that are derived from the mRNA sequenced in the proximity of the cap site, and their mapping onto unique genomic regions identifies TSS”
• Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015, unknown): “22), are sometimes used as additional support.”
• lincRNAs: Genomics, Evolution, and Mechanisms (2013, unknown): “These include methods for highresolution mapping of transcription start sites, e.g., using cap analysis of gene expression (CAGE) (Kodzius et al., 2006), and genome-wide annotation of polyadenylation sites, e.g., using 3P-seq (Jan et al., 2011; Ulitsky et al., 2012) (Figure 1A).”
• The Landscape of long non-coding RNA classification (2015, unknown): “Cap assisted gene expression (CAGE): a transcriptome profiling procedure that targets RNAs with a 5′-cap [144].”
• Modeling gene expression using chromatin features in various cellular contexts (2012, unknown): “Moreover, gene expression levels were quantified in two forms: RNA-Seq [15] was used to quantify transcript (Tx)-based expression levels; and CAGE [16,17] and 5’ tags of RNA-PET [18] were used to capture transcription start site (TSS)-based expression levels [19].”