TRANSCRIPTOME 2002: From Functional Genomics to Systems
Characterization of the Upstream Regions of 836 Orthologous Human/Mouse Genes
Mihaela Zavolan1, Terry Gaasterland1, and Nikolaus Rajewsky2, 1Laboratory for Computational Genomics, The Rockefeller University, New York, NY, 2Center for Studies in Physics and Biology, The Rockefeller University, New York, NY
In recent years, it has been become evident that cross species comparisons are a very powerful tool for discovering functional regions in genomic DNA [1-4]. For example, regulatory elements such as binding sites for transcription factors are frequently found in conserved parts of upstream sequences. In order to study the conservation of upstream sequences on a genome--wide level, we have developed a fully automated computational pipeline to identify pairs of orthologous genes, to unambiguously map them to the corresponding genomic sequences, to isolate their upstream regions, and to identify conserved sequence elements. Starting with the RefSeqdatabase  of mouse and human protein sequences, this pipeline extracted data for 836 pairs of orthologous human/mouse genes. We present the analysis of the sequence composition, degree of conservation, and presence of regulatory motifs in the upstream region of these genes.
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