The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
Open accessAbstract
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5′ end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Using the transcriptome to annotate the genome
Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E. (2002) · Nature Biotechnology · doi:10.1038/nbt0502-508 · Cited by 630
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RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
CpG islands and the regulation of transcription
Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187
Long non-coding RNAs: new players in cell differentiation and development
Fatica, A., & Bozzoni, I. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3606 · Cited by 2,980
Opportunities and obstacles for deep learning in biology and medicine
Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0387 · Cited by 2,310
Metadata
- Authors
- Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M., Arakawa, T., Fukuda, S., Sasaki, D., Podhajska, A., Harbers, M., Kawai, J., Carninci, P., & Hayashizaki, Y.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2003-12-08
- Volume
- 100
- Issue
- 26
- Pages
- 15776-15781
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2114703458
- Cited by
- 773
- References
- 3
- FWCI
- 6.11
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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