Data Integration and Target Selection for Medicago Genomics

Abstract

A large collection of expressed sequence tags (ESTs) have been generated for Medicago truncatula. With the progress of genome sequencing, M. truncatula has become a model legume for genomics. However, the sequence and related information is distributed across several sites, and thus not organized in an optimal way for genomic studies. We developed computational methods to transform, clean and load the sequence data into a local warehouse, and to integrate the data with other information from major public databases (e.g. GenBank, Pfam and PDB). The integrated database system allows us to build web-based tools for genomics target selection. For our own research, the system permits a genome-wide search for genes that may be involved in legume-specific biological processes. The database and related bioinformatic tools are available at http://bioinfo.noble.org/.

Aphid Feeding Activates Expression of a Transcriptome of Oxylipin-based Defense Signals in Wheat Involved in Resistance to Herbivory

“…The CEDA virtual subtraction procedure (Wang and Zhang 2004) was applied to the data in Table 2 to identify genes uniquely expressed in Dnx infested plants or Dn0 infested plants. This was accomplished by using the formulae [( Dnx infested- Dnx control)-( Dn0 infested- Dn0 control)] for Dnx plants, and [( Dn0 infested- Dn0 control)-( Dnx infested- Dnx control)] for Dn0 plants.…”

“…Comparisons of changes in differential up- or downregulation of gene expression between RWA-infested Dnx and Dn0 plants were discriminated by using the CEDA (Comparative EST Data Analysis) virtual subtraction procedure developed by Wang and Zhang (2004). Genes expressed in uninfested control plants were removed from those in infested plants with the formula: [( Dnx infested- Dnx control)-( Dn0 infested- Dn0 control)] for Dnx plants, and [( Dn0 infested- Dn0 control)-( Dnx infested- Dnx control)] for Dn0 plants.…”