75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

95 Predicting the Redundome: A Genome-Wide View of Overlapping Gene Function
Dennis Shasha, Sunayan Bandyopadhyay 1 , Cindy Yang 2 , Kenneth Birnbaum 2
1
Courant Institute, New York University, 2 Biology Department, New York University
High throughput analysis of gene function in plants will be accelerated by three sets of resources: 1) an intricate
knowledge of when and where genes are active, 2) predictive power to define genetic redundancy, and 3) facile techniques
to knockout multiple genes and observe their phenotype. The availability of thousands of microarray experiments in
Arabidopsis has provided progress on the first resource. We use, in part, the comprehensive expression to report progress
on the second resource, predicting genetic redundancy in a model organism replete with high levels of gene duplication.
Using a training set of documented cases of redundant and non-redundant genes, we find that commonly used attributes to
determine genetic redundancy, such as sequence comparison or gene expression, are poor predictors of redundancy alone.
To address this issue, we combined a wide set of attributes for potential gene pairs in the genome, including sequence
comparison, thousands of microarray experiments, the sharing of predicted protein domains, and others. Considering
multiple attributes of gene pairs together, we have used the training set and the list of attributes to guide two machine
learning techniques -- decision trees and support vector machines -- to establish non-trivial rules to predict functional
overlap in the Arabidopsis genome. Withholding analysis shows that these rules are 75 to 80% accurate. This provides a
critical resource in devising a systematic methodology to plan multiple mutant experiments to uncover functional roles
of Arabidopsis genes.
96 Web services for Arabidopsis data integration
Dirk Haase 1 , Hank Wu 2 , Heiko Schoof 1 , Chris Town 2
1
Max-Planck-Institute for Plant Breeding Research, Cologne, Germany, 2 The Institute for Genomic Research,
Rockville MD, USA
In an international collaborative project, web services for Arabidopsis data integration are being generated using the BioMoby
platform. These will allow novel queries and analyses and are especially suited to generate custom workflows. A project web
site provides an entry point to a collection of workflows and tools to query and use the web services network. It also provides
developer resources aiming to make it easy for new data providers to join the project and develop and integrate their resources.
Online demonstrations will be available at the poster. In a scheduled workshop, progress in the project and the tools
and services available will be presented. We are very much interested in feedback and input on web services, tools or
workflows that would be important for the community, and will be collecting these at the poster and at the workshop.
http://bioinfo.mpiz-koeln.mpg.de/araws