Gene expression Expressed sequence tags

EST Expressed sequence tag. An EST is a partial sequence (typically less than 40C bases) selected from cDNA and used to identify genes expressed in a particuh tissue... 

When the Arabidopsis Expressed Sequence Tag (EST) Database was searched with the tomato fmit Psubunit protein sequence two related cDNAs were identified (Figure 11). cDNA 2 is near full length and has been completely sequenced, cDNA 1 has also been sequenced but currently lacks approximately 100 amino acids of coding region. The two Arabidopsis cDNAs are 81% identical at the protein level and have lower identity to the protein encoded by tomato gene 1, 64 and 63% for cDNA 1 and cDNA 2, respectively. However, both cDNAs encode... 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Mann, M. (1996). A shortcut to interesting human genes peptide sequence tags, expressed-sequence tags and computers. Trends Biochem. Sci. 21, 494-495. 

Tetteh, K.K.A., Loukas, A., Tripp, C. and Maizels, R.M. (1999) Identification of abundantly-expressed novel and conserved genes from infective stage larvae of Toxocara canis by an expressed sequence tag strategy. Infection and Immunity 67, 4771-4779. 

Ewing B et al. Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genet 2000 25 232-234. 

Ulrich CM, Bigler J, Velicer CM et al. Searching expressed sequence tag databases discovery and confirmation of a common polymorphism in the thymidylate synthase gene. Cancer Epidemiol Biomarkers Prev 2000 9 1381-1385. 

Expressed sequence tag (EST) analysis of cDNAs from specific plant tissues has proved to be a valuable tool for the identification of genes for secondary metabolite biosynthesis.36 We have used this approach to identify two distinct sequences predicted to encode OSCs from cDNA libraries from roots of diploid oat (Avena strigosa).35 One of these sequences is highly homologous to cycloartenol... 

Figure 11.2 Gene Ontology assignments of the M. truncatula expressed sequence tags.

Holman, M.A. and S. Munzer, "Intellectual Property Rights in Genes and Gene Fragments A Registration Solution for Expressed Sequence Tags," Iowa L. Rev., 85, 735-848 (2000). 

PMF is generally used to identify proteins that have been previously separated by 2-D GE so that additional information including the molecular weights and isoelectric points can be used to supplement PMF identification. PMF is not well suited for searching expressed sequence tag (EST) databases that contain incomplete gene coding information for particular ESTs and it is not adequate for the analysis of complex protein mixtures in solution. 

Mao WH, Shi K, Gong YM, Xia XJ, Zhang YP, Zhou YH, Yu J (2007) Screening genes associated with autotoxicity in Cucumis sativus L roots using expressed sequence tags. Allelopathy J 20 355-362... 

Rea G, Metoui O, Infantino A, Federico R, Angelini R (2002) Copper amine oxidase expression in defense responses to wounding and Ascochyta rabiei invasion. Plant Physiol 128 865-875 Roeder V, Collen J, Rousvoal S, Corre E, Leblanc C, Boyen C (2005) Identification of stress gene transcripts in Laminaria digitata (Phaeophyceae) protoplast cultures by Expressed Sequence Tag analysis. J Phycol 41 1227-1235... 

Expressed Sequence Tags and In Silico Methods Expressed sequence tags (ESTs) are short nucleotide sequences of complementary DNA with about 200-500 base pairs. They are parts of the DNA that code for the expression of particular proteins. EST sequencing provides a rapid method to scan for all the protein coding genes and to provide a tag for each gene on the genome. 

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

Potato type II (Potll) inhibitors are disulfide-rich peptides of approximately 50 amino acids in size. They were first discovered in leaves, seeds, and other organs of Solanaceae and are a source of much interest as plant defense proteins. Recently, Barta et analyzed expressed sequence tag (EST) and genomic data and discovered 11 genes that code for Potll inhibitors in various monocotyledonous and dicotyledonous plants. Potll inhibitors are expressed as large precursor proteins that contain up to eight sequence repeats of the inhibitor precursor. In one particularly fascinating case from the ornamental tobacco (N. data), the precursor adopts a circular permuted structure.Barta et al. observed that genes outside the Solanaceae family seem... 

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