Linking microarray reporters with protein functions

Background: The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results: This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. A. Evelo
• Keywords: BMCBI 2007, Microarray Reporter, Reporter, Reporter Sequences