Poster #RP110
Arabidopsis Functional Genomics Data Integration
Nicolas Tsesmetzis*, Matthew Couchman*, Sean Walsh*
*John Innes Centre, Norwich, UK
Our group is currently working on two systems:
The first one is the Arabidopsis thaliana Integration Database (http://atidb.org). ATIDB integrates the latest arabidopsis gene models and annotation with the location of insertional mutagens, GO annotation, small RNA locations, InterProScan results, primer locations, etc. Apart from providing a browsing and search interface, ATIDB allows sophisticated queries and reporting. We are working on extending ATIDB to include whole genome tiling array results, promoter locations and protein-protein interactions.
The second system is the Arabidopsis Reactome. A knowledge-base that models biological processes as a series of events and it is based on the human Reactome data-structure (http://www.reactome.org). The Arabidopsis Reactome instance will have many scientific applications once fully established:
As a reference on the state of knowledge
For overlaying "-omics" data in order to visualise sets of entities (genes, proteins, metabolites) involved in certain processes
Establish a high quality reference genome for the rapid annotation of function in newly sequenced plant genomes
As a basis for systems biology applications (parameter estimation in metabolic flux analysis, search for common network motifs etc).
Both the Arabidopsis Reactome and ATIDB are available under open source terms.