title: Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.
abstract: BACKGROUND
  High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing).
  
  
  RESULTS
  The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery.
  
  
  CONCLUSIONS
  Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.
authors.affiliation: Department of Tumor Biology, Rikshopitalet-Radiumhospitalet Medical Center, Montebello, Oslo, Norway. fangli@radium.uio.no
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.forename: Tor-Kristian
authors.initials: TK
authors.lastname: Jenssen
authors.forename: Jeff
authors.initials: J
authors.lastname: Trimarchi
authors.forename: Claudio
authors.initials: C
authors.lastname: Punzo
authors.forename: Connie L
authors.initials: CL
authors.lastname: Cepko
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
authors.forename: Winston Patrick
authors.initials: WP
authors.lastname: Kuo
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D051379:Mice; D008810:Mice, Inbred C57BL; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*