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Annotating regulatory DNA based on man-mouse genomic comparison

MPS-Authors

Dieterich,  Christoph
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50128

Cusack,  Brian
Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

Wang,  Haiyan
Max Planck Society;

Rateitschak,  Katja
Max Planck Society;

Krause,  Antje
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50613

Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Dieterich, C., Cusack, B., Wang, H., Rateitschak, K., Krause, A., & Vingron, M. (2002). Annotating regulatory DNA based on man-mouse genomic comparison. Proceedings of the European Conference on Computational Biology (ECCB 2002), S84-S90.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-8BE4-8
Abstract
Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such conserved elements from upstream regions of orthologous gene pairs from man and mouse. We focus on orthologous genes in order to maximize our chances to find functionally similar regulatory elements. The identification of conserved elements is effected using the Waterman–Eggert local suboptimal alignment algorithm. We have modified an implementation of this algorithm such that it integrates the determination of statistical significance for the local suboptimal alignments. This has the effect of outputting a dynamically determined number of suboptimal alignments that are deemed statistically significant. Comparison with experimentally determined annotation shows a striking enrichement of regulatory sites among the conserved regions. Furthermore, the conserved regions tend to cover the promotor region described in the EPD database.