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      SAGE-Project

      • Project Description
      • SAGE
      • Yeast - Introduction to Saccharomyces cerevisiae
      • Yeast Expression Pattern
      • References and Notes

      Project Description

      In collaboration with the Munich Information Centre for Protein Sequences (MIPS), two of our students were asked to develop a database scheme for an object-oriented databank holding SAGE expression data of yeast (Saccharomyces cerevisiae). The project also includes an algorithm for analysing the data, and a WWW-Interface to the databank.

      SAGETM (Serial Analysis of Gene Expression)

      SAGE allows the quantitative and simultaneous analysis of a large number of transcripts, without the prerequisite of a hybridization probe for each transcript. SAGE technology is based on two principles. First a short sequence tag (10 -14 bp) is generated that contains sufficient information to identify uniquely a transcript, provided that it is derived from a defined location within that transcript. Second, many transcript tags can be concatenated into a single molecule and then sequenced, revealing the identity of multiple tags simultaneously. The expression pattern of any population of transcripts can be quantitativley evaluated by determining the abundance of individual tags and identifying the gene corresponding to such tag. The SAGE-Query permits you to search in the yeast SAGE database holding SAGE expression data. For more detailed information about the SAGE-technology ( developed by Bert Vogelstein, Ken Kinzler, and Victor Velculescu at the Johns Hopkins University Oncology Center. (Patent No.5,695,937)) and futher SAGE references, please visit the following links:

      • Genzyme Corporation: SAGE-Technology
      • Johns Hopkins Oncology Center: SAGE

      Yeast - A short introduction to S.cerevisiae

      Yeast (Saccharomyces cerevisiae), better known as brewers or bakers yeast is a simple, unicellular eukaryote. Yeast is a useful organism for biological research because of its useful features:

      • cheap and easy cultivation.
      • short generation times.
      • insensitive and easy to manipulate by molecular techniques.
      • powerful eukaryote model system.
      • well characterized genetic and biochemical knowledge (accumalated in many years).

      A lot of features (genetic, biochemical-pathways) have been found in yeast that are similar to that of higher organism. This characteristics make S.cerevisiae to a useful model system for genetic and biochemical research. The determination of the sequence S. cerevisiae can be a reference towards the sequence of the human or other higher eukaryotic genes, and in April 1996, the genome Yeast Sequencing Project finished it. More than 100 laboratories from Europe, USA, Canada and Japan took part of this Yeast Genome Project. S.cerevisiae contains a haploid set of 16 chromosomes, ranging in size of 200 to 2,000 kb, including more than 13 million bases. The DNA sequences (nuclear and mitochondrial genome) were analysed by the Munich Information Centre for Protein Sequences (MIPS). Mips analysed 6275 ORF (Open Reading Frames), 87 ORFs smaller than 100 amino acids (nuclear genome). The analysis of the mitochondrial genome results 32 ORFS (4 smaller than 100 aminoacids). For detailed description, please look at the MIPS-Homepage, other links and References.

      Yeast Expression Pattern

      SAGE-technology provide quantitative gene expression data and demonstrate the feasibility of genome-wide expression studies in eukaryotes. SAGE was used to identify a set of genes expressed from the S.cerevisiae genome under limited physiological conditions (glucose/fatty acid). An object-oriented database holding these limited data and the WWW-Interface allows you to query the yeast SAGE data. Possible queries are:

      • query by a Tagsequenz.
      • query by a Genname.
      • query by a ORF-Name.

      The existing database holds SAGE expression data that were integrated with the existing positional information of the yeast genome (sequenzed Yeast Genome, known and unknown Gene- and ORF information. A dynamic HTML page accepts retrieval information from the user, search an existing database, and generate an answer on the fly. The CGI (Common Gateway Interface) protocol defines how the server communicates with these programs. A Tag-Query represent a 10 bp SAGE tag correponding to a sequence in the yeast genome; Gene-Query represents the gene or genes corresponding to a particular tag; ORF-Query represents Locus and Description of the ORF-Name and the functional description of each ORF.

      REFERENCES AND NOTES

      SAGE-References:

    • Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995). Serial Analysis Of Gene Expression. Science 270, 484-487.
    • Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., and Kinzler, K. W. (1997). Characterization of the yeast transcriptome. Cell 88, 243-251.

      SAGE-Links:

    • Genzyme Corporation: SAGE-Technology
    • Johns Hopkins Oncology Center: SAGE

      Yeast-Reference:

    • F. Sherman, Yeast genetics. The Encyclopedia of Molecular Biology and Molecular Medicine, pp.302-325, Vol. 6. Edited by R. A. Meyers, VCH Pub., Weinheim, Germany,1997.

      Yeast-Databases and further information about yeast:

    • MIPS Yeast Genome Project Page
    • Saccharomyces Genome Database (SGD)

      This Project Homepage is under development; a temporary report about the project is available (in german only).

      Andre Lewin (alewin@techfak.uni-bielefeld.de)
      Marin Bennemann (mbennema@techfak.uni-bielefeld.de)
      Oct 1998


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