All the cases in the database were analysed using the South Asian Name and Group Recognition Algorithm SANGRAA).
In addition, this tool has been used to find crop-specific and new traits, and as a test case, 150 traits of the IMIS database were analysed using the subset maize trait ontology (CO_322) and TO; 74 traits were matched to those of maize trait ontology and 35 to those of TO (Fig. 2).
To obtain a final annotation table, the annotations from each database were analysed using the BLAST scoring system [ 62] to obtain the best annotation for each transcript.
The 7,353 protein sequences from the global assembly that exhibit homology in the protein databases were analysed using a new integrative functional annotation pipeline (Gagnière et al., manuscript in preparation).
The database of promoters was analysed using MEME to identify conserved motifs.
The resulting data was analysed using the Swiss-Prot database (Swiss-Prot group, Switzerland).
The DEG gene list (of 5345 genes) was analysed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) for pathway analysis.
The expression of La mRNA in human lung cancer samples was analysed using the online database Oncomine, and the protein expression of La was examined using a TissueFocus Cancer Survey Tissue Microarray.
This was analysed using the KEGG database [ 44].
The functional significance of differentially expressed genes was analysed using the 'Database for Annotation Visualization and Integrated Discovery' (DAVID) (http://david.abcc.ncifcrf.gov).abcc.ncifcrf.gov
