summary
Serial analysis of gene expression (SAGE) is a powerful technique for measuring global gene expression through sampling of transcript tags. SAGE tag collections or libraries serve as a rich data source for differential gene expression analysis, transcriptome mapping, and gene discovery. Transcriptome mapping and gene discovery are facilitated by extensions of SAGE, e.g., Long SAGE, where the transcript tags are elongated by utilization of a different tagging enzyme. SAGE, as a sequencing-based technique, is prone to errors resulting in artifact SAGE tag sequences and erroneous tag numbers. A methodology to pinpoint and correct tag artifacts is necessary to fully exploit the value of large SAGE libraries.
SAGEScreen is a tag sequence correction algorithm. The algorithm is a multistep procedure that addresses error rates and performs ditag and tag processing. The error rate estimates are based on a stochastic model of PCR and sequencing related mutations. The ditag processing step is essential for calculation of unbiased tag numbers, and the tag processing step allows for filtration of tag sequence artifacts and adjustment of tag numbers.
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Reference
Lash, A. E., Tolstoshev, C. M., Wagner, L., et al. (2000) SAGEmap: a public gene expression resource. Genome Res. 10, 1051–1060.
Matsumura, H., Ito, A., Saitoh, H., et al. (2005) SuperSAGE. Cell Microbiol. 7, 11–8.
Saha, S., Sparks, A. B., Rago, C., et al. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–12.
Akmaev, V. R. and Wang, C. J. (2004) Correction of sequence-based artifacts in serial analysis of gene expression. Bioinformatics 20, 1254–1263.
Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–85.
Atkinson, K. E. (1988) An Introduction to Numerical Analysis. 2nd ed. John Wiley & Sons, New York, NY.
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© 2008 Humana Press, a part of Springer Science+Business Media, LLC
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Akmaev, V.R. (2008). Correction of Technology-Related Artifacts in Serial Analysis of Gene Expression. In: Nielsen, K.L. (eds) Serial Analysis of Gene Expression (SAGE). Methods in Molecular Biology™, vol 387. Humana Press. https://doi.org/10.1007/978-1-59745-454-4_10
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DOI: https://doi.org/10.1007/978-1-59745-454-4_10
Publisher Name: Humana Press
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