Gene Expression

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Functional genomics is defined as the use of molecular biological tools to explore the gene functions and interactions from genome sequencing data (SERC, 2013). Expressed Sequence Tag (EST) and Serial Analysis of Gene Expression (SAGE) are among the techniques that are commonly used in functional genomics. The goal of transcriptome studies is to identify the transcripts expressed in a genome. Since human genome studies, EST was the main technique used for transcript identification. Recently, SAGE has been widely used in transcriptome analysis. ESTs are short, single pass and randomly selected cDNA sequences derived from library clones (Nagaraj, Gasser & Ranganathan, 2006). SAGE is a quantitative and direct method of analyzing gene expression without prior knowledge of the genes (Yamamoto, Wakatsuki, Hada & Ryo, 2001). Although both EST and SAGE are applied in studying functional genomics, they have different approaches. Sun et al. (2004) stated that EST method is based on single transcript, single clone and single sequencing approach whereas SAGE is based on multiple transcripts, multiple tags, single clone and single sequencing approach, resulting in each SAGE sequence representing multiple transcripts.

Basic Principles of EST and SAGE

Nagaraj et al. (2006) mentioned that EST analysis contains several steps and there are various tools available to obtain biological information from the analysis. The basic principles of EST is messenger RNA (mRNA) sequences to represent duplicates from expressed genes, cDNA libraries created from various cells and tissues, single pass sequencing of both ends of insert and accumulation of readable sequence part in EST database. In order to generate EST, RNA are first reverse transcr...

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Patino, W. D., Milan, O. Y., & Hwang, P. M. (2002). Serial analysis of gene expression. Circulation Research, 91, 565-569.

Science Education Resource Center. (2013). Functional genomics: Strategies for testing and extending genomics data at the bench. Retrieved from genomics/chamaecrista/functional_geno.html.

Sun, M., Zhou, G., Lee, S., Chen, J., Shi, R. Z., & Wang, S. M. (2004). SAGE is far more sensitive than EST for detecting low abundance transcripts. BMC Genomics, 5(1), 1-4.

Tuteja, R., & Tuteja, N. (2004). Serial analysis of gene expression: Applications in human studies. Journal of Biomedicine and Biotechnology, 2, 113-120.

Yamamoto, M., Wakatsuki, T., Hada, A., & Ryo, A. (2001). Use of serial analysis of gene expression (SAGE) technology. Journal of Immunological Methods, 250, 45-66.
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