Bioinformatics Preprint 04-017
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Titel:
Comparative promoter region analysis powered by CORG
Author(s):
Christoph Dieterich,
Steffen Grossmann,
Andrea Tanzer,
Stefan Ropcke,
Peter F Arndt,
Peter F Stadler,
Martin Vingron
Submitted for publication in:
BMC Genomics
Abstract:
Background: Promoters are key players in gene regulation. They
receive signals from various sources (e.g. cell surface receptors) and
control the level of transcription initiation, which largely determines
gene expression. In vertebrates, transcription start sites and surrounding
regulatory elements are often poorly defined. To support promoter analysis,
we present CORG (http://corg.molgen.mpg.de), a
framework for studying upstream regions including untranslated
exons.
Methods: The automated annotation of promoter regions integrates
information of two kinds. First, it detects cross-species conservation
within upstream regions of orthologous genes. Pairwise as well a multiple
sequence comparisons are computed. Second, binding site descriptions
(position-weight matrices) are employed to predict conserved regulatory
elements. Assembled EST sequences and verified transcription start sites
are incorporated to distinguish exonic from other sequences. Results: As of
now, we have included 5 species in our analysis pipeline (man, mouse, rat,
fugu and zebrafish). We characterized promoter regions of 16,127 groups of
orthologous genes. All data are presented in an intuitive way via our
website or can be directly accessed via our DAS server
http://tomcat.molgen.mpg.de:8080/das. The benefits of our framework are
exemplarily shown in the context of phylogenetic profiling of transcription
factor binding sites and detection of microRNAs close to transcription
start sites of our gene set. Conclusions: The CORG platform is a versatile
tool to support analyses of gene regulation in vertebrate promoter
regions. Applications for CORG cover a broad range from studying evolution
of DNA binding sites and promoter constitution to the discovery of new
sequence elements (e.g. microRNAs and binding sites).
Keywords:
CORG database,
promoter regions,
transcription factor binding sites,
micro RNAs
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