title: Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data.
abstract: BACKGROUND
  The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset is precisely linked to a gene, and probeset intensity is interpreted as gene expression. The increased knowledge that one gene may have multiple transcript variants clearly brings up the necessity of updating this gene-level annotation to a refined transcript-level.
  
  
  RESULTS
  Through performing rigorous alignments of the Affymetrix probe sequences against a comprehensive pool of currently available transcript sequences, and further linking the probesets to the International Protein Index, we generated transcript-level or protein-level annotation tables for two popular Affymetrix expression arrays, Mouse Genome 430A 2.0 Array and Human Genome U133A Array. Application of our new annotations in re-examining existing expression data sets shows increased expression consistency among synonymous probesets and strengthened expression correlation between interacting proteins.
  
  
  CONCLUSIONS
  By refining the standard Affymetrix annotation of microarray probesets from the gene level to the transcript level and protein level, one can achieve a more reliable interpretation of their experimental data, which may lead to discovery of more profound regulatory mechanism.
authors.affiliation: Shanghai Center for Bioinformation Technology, Shanghai, PR China. yuhui@scbit.org <yuhui@scbit.org>
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Kang
authors.initials: K
authors.lastname: Tu
authors.forename: Lu
authors.initials: L
authors.lastname: Xie
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Li
authors.forename: Yi-Xue
authors.initials: YX
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D015342:DNA Probes; D014157:Transcription Factors