Agilent Barley Gene Expression Microarray Reannotation

An attempt was made to reannotate as many sequences as possible in the Agilent Barley Gene Expression Microarray, 4x44K, based on the UniProt plant protein collection and the Gramene rice genome annotation. After downloading the full sequences of the array oligos from the Core and EST sections of the NCBI Nucleotide Archive, the TIGR Plant Transcript Assembly and the DFCI Gene Indices collection, which were not provided with the array annotation, a search was made for possible homologs in the 2 February 2011 UniProt Knowledgebase Plant section and the Gramene rice genome assembly, version MSU6. A BLAST search was run with default parameters, the only modification being the use of the query sequence filtering for low complexity regions. After the BLAST search, the results were filtered, choosing the one with the best score, but requiring an e-value lower than 1e-30 and an overall fraction of iden- tical positions across the hit and query alignment of at least 50%. The description and GeneOntology (GO) associations were reannotated for all array oligos where a suitable homolog was found either in UniProt or in the Gramene database. The file contains the full sequence collection from which the array probes were derived, the Molecular function, Biological process and Cellular compartment Gene Ontology annotations in BiNGO (http://apps.cytoscape.org/apps/bingo) format and the annotation table with the UniProt and Gramene hits in a tab delimited file.