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Regulatory Interaction Maps of Arabidopsis Seed Development

RIMAS - Regulatory Interaction Maps of Arabidopsis Seed Development

Embryogenesis and seed formation involve a multitude of highly interconnected developmental processes which are precisely controlled by a complex network of genetic pathway regulators. In Arabidopsis, seed development and maturation are regulated by the LEC1/AFL-B3 network of transcription factors consisting of the central factor LEC1 and the AFL-B3 factors ABI3, FUS3 LEC2 which share the highly conserved B3 domain.

RIMAS presents detailed network diagrams which reflect the interactions of these transcription factor hierarchies, gene promoter elements, hormonal pathways, epigenetic processes and chromatin remodelling and provide an easy access to the relevant references.

RIMAS network nomenclature is based on the agreed-upon convention for the display and handling of biological regulatory networks designated as Systems Biology Graphical Notation ( SBGN, Le Novère et al., 2009, Nature Biotech., 27, 735).

RIMAS is a web-based information portal and provides a comprehensive regularly updated overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development. The service provides access to standardized network diagrams, linked literature databases and possibilities to export diagrams in common exchange formats such as GML for modifying network layouts according to individual purposes and further application using tools such as VANTED ( VANTED, Björn H. Junker, Christian Klukas and Falk Schreiber, 2006, BMC Bioinformatics, 7:109) or other image formats.

RIMAS invites the feed back of all researchers in the field in order to update the current data and reference collection and to develop the website into a platform of intense discussion about embryo and seed development as well as about the application of SBGN for the representation of biological networks.

How to cite RIMAS:
Junker A., Hartmann A., Schreiber F. and Bäumlein H., (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6):303-307.