Discover where genes are and how highly they are being expressed

[Denis Jacob Machado]

Hi!

There are several techniques that can provide evidence for where genes are and how highly they are being expressed. The most well-know of these techniques propably are: ESTs, SAGE, CAGE, RACE, MPSS, and RNA-Seq.

Here some articles explaining each one of those techniques:

ESTs
Nagaraj, S. H., Gasser, R. B., & Ranganathan, S. (2007). A hitchhiker’s guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics, 8(1), 6–21. doi:10.1093/bib/bbl015

Readers might also be interested in this collection of software tools for EST pre-processing, clustering and assembly, database matching and functional annotation: http://biolinfo.org/EST

SAGE
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995). Serial analysis of gene expression. Science (New York, N.Y.), 270(5235), 484–487. doi:10.1126/science.270.5235.484

Also, check this very simple and informative blog post with five steps to SAGE and a list of the problems with gene tags: http://www.scq.ubc.ca/painless-gene-expression-profiling-sage-serial-analysis-of-gene-expression/

CAGE
Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., … Hayashizaki, Y. (2003). Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proceedings of the National Academy of Sciences of the United States of America, 100(26), 15776–15781. doi:10.1073/pnas.2136655100

RACE
Schaefer, B. C. (1995). Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends. Analytical Biochemistry. doi:10.1006/abio.1995.1279
Zhang, Y. (1988). Rapid Amplifi cation of cDNA Ends (Vol. 221, pp. 13–25).

MPSS
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D. H., Johnson, D., … Corcoran, K. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18(6), 630–634. doi:10.1038/76469
Reinartz, J., Bruyns, E., Lin, J. Z., Burcham, T., Brenner, S., Bowen, B., … Woychik, R. (2002). Technique review massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Briefings in Functional Genomics and Proteomics, 1(1), 95–104. doi:10.1093/bfgp/1.1.95

RNA-Seq/ WTSS
Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57–63.
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008). RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18(9), 1509–1517. doi:10.1101/gr.079558.108

Articles will be temporally available here.

BW, D