Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data

BMC Bioinformatics. 2007 Jun 11;8:194. doi: 10.1186/1471-2105-8-194.

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.

Conclusion: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • DNA Probes / genetics*
  • Databases, Genetic*
  • Gene Expression Profiling / methods*
  • Information Storage and Retrieval
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis / methods*
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Transcription Factors / genetics*

Substances

  • DNA Probes
  • Transcription Factors