ACM transactions on information systems (January) by Association for Computing Machinery PDF

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We have developed preprocessing methodologies to address problems in analyzing SAGE data due to noise caused by sequencing error, normalization methodologies to account for libraries sampled at different depths, and missing tag imputation methodologies to aid in the analysis of poorly sampled SAGE libraries. We have also used subspace selection using the Wilcoxon rank sum test to exclude tags that have similar expression levels regardless of source. Using these methodologies we have clustered, using the OPTICS algorithm, 88 SAGE libraries derived from cancerous and normal tissues as well as cell line material.

Gene expression is the process of making so-called messenger RNA (mRNA) copies of a gene (a part of the DNA strand of the cell). mRNA, which is essentially a sequence of four bases denoted by A, C, G, and T, is then translated in the cell into an amino acid sequence that forms the basis of a protein. Each tissue type in an organism requires different amounts of different proteins to perform its duties. The amount of a particular protein produced by a cell is partly controlled by the number of corresponding mRNA copies.

1993. Compression of DNA sequences. In Proceedings of the Data Compression Conference. 340–350. GRUMBACH, S. AND TAHI, F. 1994. A new challenge for compression algorithms: Genetic sequences. J. Inform. Process. Manage. 30, 6, 875–886. , AND YANG, E. 2000. Estimating DNA sequence entropy. In 11th Annual ACMSIAM Symposium on Discrete Algorithms. 409–418. , AND ZHANG, H. 2001. An information based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17, 149–154.

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ACM transactions on information systems (January) by Association for Computing Machinery


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